5-Methyl-Tetrahydrofolate and the S-Adenosylmethionine Cycle in C57BL/6J Mouse Tissues: Gender Differences and Effects of Arylamine N-Acetyltransferase-1 Deletion

Folate catabolism involves cleavage of the C⁹-N¹⁰ bond to form p-aminobenzoylgluamate (PABG) and pterin. PABG is then acetylated by human arylamine N-acetyltransferase 1 (NAT1) before excretion in the urine. Mice null for the murine NAT1 homolog (Nat2) show several phenotypes consistent with altered folate homeostasis. However, the exact role of Nat2 in the folate pathway in vivo has not been reported. Here, we examined the effects of Nat2 deletion in male and female mice on the tissue levels of 5-methyl-tetrahydrofolate and the methionine-S-adenosylmethionine cycle. We found significant gender differences in hepatic and renal homocysteine, S-adenosylmethionine and methionine levels consistent with a more active methionine-S-adenosylmethionine cycle in female tissues. In addition, methionine levels were significantly higher in female liver and kidney. PABG was higher in female liver tissue but lower in kidney compared to male tissues. In addition, qPCR of mRNA extracted from liver tissue suggested a significantly lower level of Nat2 expression in female animals. Deletion of Nat2 affected liver 5- methyl-tetrahydrofolate in female mice but had little effect on other components of the methionine-S-adenosylmethionine cycle. No N-acetyl-PABG was observed in any tissues in Nat2 null mice, consistent with the role of Nat2 in PABG acetylation. Surprisingly, tissue PABG levels were similar between wild type and Nat2 null mice. These results show that Nat2 is not required to maintain tissue PABG homeostasis in vivo under normal conditions.     

Human NAT10 Is an ATP-dependent RNA Acetyltransferase Responsible for N4-Acetylcytidine Formation in 18 S Ribosomal RNA (rRNA)

Human N-acetyltransferase 10 (NAT10) is known to be a lysine acetyltransferase that targets microtubules and histones and plays an important role in cell division. NAT10 is highly expressed in malignant tumors, and is also a promising target for therapies against laminopathies and premature aging. Here we report that NAT10 is an ATP-dependent RNA acetyltransferase responsible for formation of N⁴-acetylcytidine (ac⁴C) at position 1842 in the terminal helix of mammalian 18 S rRNA. RNAi-mediated knockdown of NAT10 resulted in growth retardation of human cells, and this was accompanied by high-level accumulation of the 30 S precursor of 18 S rRNA, suggesting that ac⁴C1842 formation catalyzed by NAT10 is involved in rRNA processing and ribosome biogenesis.     

Conformational Preferences of Modified Nucleoside N(4)-Acetylcytidine, ac4C Occur at “Wobble” 34th Position in the Anticodon Loop of tRNA

Conformational preferences of modified nucleoside, N(4)-acetylcytidine, ac⁴C have been investigated using quantum chemical semi-empirical RM1 method. Automated geometry optimization using PM3 method along with ab initio methods HF SCF (6-31G**), and density functional theory (DFT; B3LYP/6-31G**) have also been made to compare the salient features. The most stable conformation of N(4)-acetyl group of ac⁴C prefers “proximal” orientation. This conformation is stabilized by intramolecular hydrogen bonding between O(7)···HC(5), O(2)···HC2′, and O4′···HC(6). The “proximal” conformation of N(4)-acetyl group has also been observed in another conformational study of anticodon loop of E. coli elongator tRNA^Met. The solvent accessible surface area (SASA) calculations revealed the role of ac⁴C in anticodon loop. The explicit molecular dynamics simulation study also shows the “proximal” orientation of N(4)-acetyl group. The predicted “proximal” conformation would allow ac⁴C to interact with third base of codon AUG/AUA whereas the ‘distal’ orientation of N(4)-acetyl cytidine side-chain prevents such interactions. Single point energy calculation studies of various models of anticodon–codon bases revealed that the models ac⁴C₍₃₄₎(Proximal):G₃, and ac⁴C₍₃₄₎(Proximal):A₃ are energetically more stable as compared to models ac⁴C₍₃₄₎(Distal):G₃, and ac⁴C₍₃₄₎(Distal):A₃, respectively. MEPs calculations showed the unique potential tunnels between the hydrogen bond donor–acceptor atoms of ac⁴C₍₃₄₎(Proximal):G₃/A₃ base pairs suggesting role of ac⁴C in recognition of third letter of codons AUG/AUA. The “distal” conformation of ac⁴C might prevent misreading of AUA codon. Hence, this study could be useful to understand the role of ac⁴C in the tertiary structure folding of tRNA as well as in the proper recognition of codons during protein biosynthesis process.     

Conformation of N4-acetylcytidine,a modified nucleoside of tRNA,and stereochemistry of codon-anticodon interaction

The crystal structure of N⁴-acetylcytidine (ac⁴C) a modified nucleoside of tRNA, has been determined from three-dimensional x-ray diffractometer data. The N⁴-substituent is proximal to C(5), quite contrary to expectations from solution studies of N⁴-methylcytosine. This orientation of the N⁴-substituent will not block Watson-Crick base pairing for reading the third codon by tRNA_M^Met, and hence the discriminatory function suggested for ac⁴C might arise due to non-standard conformation of the polynucleotide backbone of the anticodon around the Wobble base. A common characteristic of the modified nucleosides that occur at the Wobble position is their inability to shield the Watson-Crick base pairing sites; this is quite consistent with the necessity for reading the third base of the codon. This is in sharp contrast to the modifications of the nucleosides adjacent to the 3′-end of anticodons, all of which prevent Watson-Crick base pairing.     

Probing small ribosomal subunit RNA helix 45 acetylation across eukaryotic evolution

NAT10 is an essential enzyme that catalyzes N⁴-acetylcytidine (ac⁴C) in eukaryotic transfer RNA and 18S ribosomal RNA. Recent studies suggested that rRNA acetylation is dependent on SNORD13, a box C/D small nucleolar RNA predicted to base-pair with 18S rRNA via two antisense elements. However, the selectivity of SNORD13-dependent cytidine acetylation and its relationship to NAT10’s essential function remain to be defined. Here, we demonstrate that SNORD13 is required for acetylation of a single cytidine of human and zebrafish 18S rRNA. In-depth characterization revealed that SNORD13-dependent ac⁴C is dispensable for human cell growth, ribosome biogenesis, translation and development. This loss of function analysis inspired a cross-evolutionary survey of the eukaryotic rRNA acetylation ‘machinery’ that led to the characterization of many novel metazoan SNORD13 genes. This includes an atypical SNORD13-like RNA in Drosophila melanogaster which guides ac⁴C to 18S rRNA helix 45 despite lacking one of the two rRNA antisense elements. Finally, we discover that Caenorhabditis elegans 18S rRNA is not acetylated despite the presence of an essential NAT10 homolog. Our findings shed light on the molecular mechanisms underlying SNORD13-mediated rRNA acetylation across eukaryotic evolution and raise new questions regarding the biological and evolutionary relevance of this highly conserved rRNA modification.     

Dual role of histone variant H3.3B in spermatogenesis: positive regulation of piRNA transcription and implication in X-chromosome inactivation

The histone variant H3.3 is encoded by two distinct genes, H3f3a and H3f3b, exhibiting identical amino-acid sequence. H3.3 is required for spermatogenesis, but the molecular mechanism of its spermatogenic function remains obscure. Here, we have studied the role of each one of H3.3A and H3.3B proteins in spermatogenesis. We have generated transgenic conditional knock-out/knock-in (cKO/KI) epitope-tagged FLAG-FLAG-HA-H3.3B (H3.3B^HA) and FLAG-FLAG-HA-H3.3A (H3.3A^HA) mouse lines. We show that H3.3B, but not H3.3A, is required for spermatogenesis and male fertility. Analysis of the molecular mechanism unveils that the absence of H3.3B led to alterations in the meiotic/post-meiotic transition. Genome-wide RNA-seq reveals that the depletion of H3.3B in meiotic cells is associated with increased expression of the whole sex X and Y chromosomes as well as of both RLTR10B and RLTR10B2 retrotransposons. In contrast, the absence of H3.3B resulted in down-regulation of the expression of piRNA clusters. ChIP-seq experiments uncover that RLTR10B and RLTR10B2 retrotransposons, the whole sex chromosomes and the piRNA clusters are markedly enriched of H3.3. Taken together, our data dissect the molecular mechanism of H3.3B functions during spermatogenesis and demonstrate that H3.3B, depending on its chromatin localization, is involved in either up-regulation or down-regulation of expression of defined large chromatin regions.     

'Protected DNA Probes' capable of strong hybridization without removal of base protecting groups

We propose a new strategy called the ‘Protected DNA Probes (PDP) method’ in which appropriately protected bases selectively bind to the complementary bases without the removal of their base protecting groups. Previously, we reported that 4-N-acetylcytosine oligonucleotides (ac⁴C) exhibited a higher hybridization affinity for ssDNA than the unmodified oligonucleotides. For the PDP strategy, we created a modified adenine base and synthesized an N-acylated deoxyadenosine mimic having 6-N-acetyl-8-aza-7-deazaadenine (ac⁶az⁸c⁷A). It was found that PDP containing ac⁴C and ac⁶az⁸c⁷A exhibited higher affinity for the complementary ssDNA than the corresponding unmodified DNA probes and showed similar base recognition ability. Moreover, it should be noted that this PDP strategy could guarantee highly efficient synthesis of DNA probes on controlled pore glass (CPG) with high purity and thereby could eliminate the time-consuming procedures for isolating DNA probes. This strategy could also avoid undesired base-mediated elimination of DNA probes from CPG under basic conditions such as concentrated ammonia solution prescribed for removal of base protecting groups in the previous standard approach. Here, several successful applications of this strategy to single nucleotide polymorphism detection are also described in detail using PDPs immobilized on glass plates and those prepared on CPG plates, suggesting its potential usefulness.     

FANCI plays an essential role in spermatogenesis and regulates meiotic histone methylation

FANCI is an essential component of Fanconi anemia pathway, which is responsible for the repair of DNA interstrand cross-links (ICLs). As an evolutionarily related partner of FANCD2, FANCI functions together with FANCD2 downstream of FA core complex. Currently, growing evidences showed that the essential role of FA pathway in male fertility. However, the underlying mechanisms for FANCI in regulating spermatogenesis remain unclear. In the present study, we found that the male Fanci^−/− mice were sterile and exhibited abnormal spermatogenesis, including massive germ cell apoptosis in seminiferous tubules and dramatically decreased number of sperms in epididymis. Besides, FANCI deletion impaired maintenance of undifferentiated spermatogonia. Further investigation indicated that FANCI was essential for FANCD2 foci formation and regulated H3K4 and H3K9 methylation on meiotic sex chromosomes. These findings elucidate the role and mechanism of FANCI during spermatogenesis in mice and provide new insights into the etiology and molecular basis of nonobstructive azoospermia.Subject terms: Cell death, Spermatogenesis     

Monitoring in vivo function of cortical microglia

Microglia, the innate immune cells of the brain, are becoming increasingly recognized as an important player both in the context of physiological brain function and brain pathology. To fulfill their executive functions microglia can modify their morphology, migrate or move their processes in a directed fashion, and modify the intracellular Ca²⁺ dynamics leading to modifications in gene expression, phagocytosis, release of cytokines and other inflammation markers, etc. Here we describe the recently developed tools enabling in vivo monitoring of morphology and Ca²⁺ signaling of microglia and show how these techniques may be used for examining microglial function in healthy and diseased brain.     

Deletion of a xenobiotic metabolizing gene in mice affects folate metabolism

The mouse arylamine N-acetyltransferase 2 (Nat2) and its homologue (NAT1) in humans are known to detoxify xenobiotic arylamines and are also thought to play a role in endogenous metabolism. Human NAT1 is highly over-expressed in estrogen receptor positive breast tumours and is implicated in susceptibility to neural tube defects. In vitro assays have suggested an endogenous role for human NAT1 in folate metabolism, but in vivo evidence to support this hypothesis has been lacking. Mouse Nat2 provides a good model to study human NAT1 as it shows similar expression profiles and substrate specificities. We have generated transgenic mice lacking a functional Nat2 gene and compared the urinary levels of acetylated folate metabolite para-aminobenzoylglutamate in Nat2 knockout and Nat2 wild-type mice. These results support an in vivo role for mouse Nat2/human NAT1 in folate metabolism. In addition, effects of the Nat2 deletion on sex ratios and neural tube development are described.     

Pushing the (nuclear) envelope into meiosis

A recent study shows that a short isoform of a mammalian nuclear lamin is important for homologous chromosome interactions during meiotic prophase in mice.Meiosis is the specialized cell division process required for sexual reproduction. As cells enter meiotic prophase, a relatively long period preceding the two chromosome divisions, nuclei and chromosomes undergo remodeling to promote interactions between homologous chromosomes. Each chromosome must find and identify its unique partner within the volume of the nucleus, a process that obviously involves large-scale chromosome movements.Over 100 years ago, cytological analysis of meiotic cells revealed a unique chromosome configuration termed the meiotic ''bouquet'', in which chromosome ends seem to be attached to the nuclear periphery, frequently in a tight cluster. The presence of the bouquet was found to coincide with the stage during which homologous chromosomes undergo pairing and synapsis. This was the first indication that interactions between the chromosomes and the nuclear envelope might be important for meiotic pairing. More recent analysis in diverse model systems has revealed that the bouquet is a consequence of interactions between chromosomes and cytoskeletal elements - microtubules or actin cables - via a protein bridge that spans the nuclear envelope. A study recently published in PLOS Genetics [1] has shed further light on the role of the nuclear lamina in meiotic progression by studying the role of a meiosis-specific isoform of a nuclear lamin protein.In metazoans the nuclear envelope is fortified by the nuclear lamina, a meshwork of intermediate filament proteins (lamins) and associated proteins that underlies the inner nuclear membrane. The lamina confers structural rigidity to nuclei and also interacts with a wide variety of nucleoplasmic, transmembrane and chromosome-associated proteins. The composition of the lamina in metazoans shows tissue-specific variability and developmental regulation. Most differentiated mammalian cells express both A-type lamins (lamins A and C, which are generated by alternative splicing of the LMNA gene) and B-type lamins (encoded by two different genes), whereas some invertebrates express only a single lamin protein. Stem cells typically lack A-type lamins, which are also dispensable for early development in mice.Among the nuclear envelope components that interact with lamins are LINC (linker of nucleoskeleton and cytoskeleton) complexes. These versatile networks involve a pair of SUN/KASH proteins that bridge both membranes of the nuclear envelope. SUN domain proteins traverse the inner membrane, with their amino termini projecting into the nucleus and their SUN domains in the lumen between the two membranes. Their partners have membrane-spanning regions adjacent to their carboxy-terminal KASH domains, short peptides that bind to the SUN domains. Using a variety of interaction modules, LINC complexes create connections between nuclear structures such as the lamina or chromosomes and cytoskeletal elements such as actin filaments or microtubules. Throughout the eukaryotes, they have essential roles in diverse processes, including the positioning and migration of nuclei within cells and anchorage of centrosomes to the nuclear envelope. During meiosis, specific LINC complexes are recruited to interact with chromosomes through the expression of meiosis-specific proteins that bind to telomeres or, less frequently, to other specialized loci [2]. These connections, probably in conjunction with meiosis-specific modifications to the cytoskeleton and motor proteins, lead to large-scale chromosome motions that facilitate homologous chromosome pairing. These movements involve dramatic motion of the LINC proteins within the nuclear membrane, sometimes involving movements of up to several micrometers that occur within a few seconds [3]. This stands in sharp contrast to the behavior of some of the same protein complexes in somatic or premeiotic cells, in which they show highly constrained motion and minimal turnover [3].In the new PLOS Genetics study [1], groups led by Manfred Alsheimer and Ricardo Benavente, both of the University of Würzburg, have now engineered a disruption of an exon in the mouse LMNA gene that is specific to the meiotic isoform lamin C2 to generate C2-deficient mice (C2^-/- mice). These collaborators have previously provided important insights into the regulation and functions of cell-type specific lamin isoforms, particularly during meiosis. Using antibodies, they characterized the lamin isoforms present in rat spermatocytes [4]. Immunolocalization revealed that a truncated isoform of lamin C (lamin C2) was localized in a patchy pattern along the nuclear envelope, along with a short B-type lamin (lamin B3) [4]. Because these short isoforms lack domains implicated in interactions between lamin subunits, they and others proposed that these proteins might form a more flexible network. This idea was supported by experiments in which meiosis-specific lamin C2 was ectopically expressed in fibroblasts and found to be more mobile within the nuclear envelope than full-length lamin C [5]. Expression of lamin C2 also resulted in aberrant localization of Sun1 in these cells. The collaborators also demonstrated that spermatogenesis was disrupted in Lmna^-/- mice, although oocyte meiosis was not obviously perturbed [6]. Although defects in meiosis-specific processes were observed in the knockout mice, it was not possible to rule out an indirect effect of lamin depletion in somatic cells on meiosis in spermatocytes, prior to the new study.An important feature of the new research [1] is that the C2^-/- mice show normal expression of all other A-type lamins. The C2^-/- males recapitulate the meiotic failure seen in Lmna^-/- mice. Nevertheless, their chromosomes frequently fail to synapse and they engage in heterologous associations or show aberrant telomere-telomere interactions; all of these defects are rare in wild-type spermatocytes. As a result of extensive apoptosis and failure of sperm maturation, the males are completely infertile. However, females are fertile, despite some evidence for pairing defects in C2^-/- oocytes.These sex-specific differences in the effects of lamin C2 loss are somewhat surprising. They could in part reflect differential implementation of meiotic checkpoints, which cull defective spermatocytes more ruthlessly than oocytes [7]. However, analysis of homologous pairing and synapsis in the C2^-/- mutant mice also revealed more severe defects in males. Both male and female mice lacking Sun1 protein are completely sterile and show synaptic failure during meiotic prophase [8]. This suggests that LINC-mediated chromosome dynamics are essential for homolog interactions during meiosis in both sexes. The milder defects caused by loss of lamin C2 in both male and female meiosis suggest that it has a less direct role in mediating chromosome movement than Sun1. This is consistent with the idea that expression of short lamin isoforms during meiosis acts primarily to increase the mobility of proteins within the nuclear envelope, relative to somatic cells. It seems likely that the dynamics of pairing, synapsis and recombination differ dramatically between spermatocytes, which are produced continually during the adult life of the male, and oocytes, which undergo meiotic prophase during fetal development. Such differences might render male meiosis more sensitive to changes in nuclear envelope organization or dynamics.The modifications made to the mouse nuclear envelope during meiosis are likely to be conserved in concept, if not in detail, in other taxa. As mentioned above, the isoforms and expression patterns of lamin proteins have diverged rapidly among the metazoa, as have the structures and functions of LINC complexes. For example, amphibians lack lamin C (and lamin C2), suggesting that its meiotic role in mammals is a recent innovation. Furthermore, the mouse Sun1 protein has a C2H2 zinc finger lacking in primate orthologs, which might suggest that it has evolved a distinct way to connect with meiotic chromosomes. It is thus not currently clear which aspects of meiotic lamina remodeling in mice can be extrapolated to other species.In Caenorhabditis elegans, meiotic chromosome dynamics are probably mediated by post-translational modification of the amino-terminal (nucleoplasmic) domain of sun-1 [9]. It is not yet known how this modification contributes to the function of the meiotic LINC complex. Direct observation has indicated that the motion of LINC complexes within the nuclear envelope becomes much less constrained as cells enter meiosis [3]. Phosphorylation of sun-1 may weaken interactions between the LINC complexes and the lamina to increase their mobility within the nuclear envelope, and/or promote interactions between LINC complexes to create high load-bearing aggregates of these proteins necessary to drive chromosome movement. It is not currently known whether the lamina itself is modified in C. elegans meiotic nuclei, but it is easy to imagine that phosphorylation could also be used to tweak protein-protein interactions within the lamina to optimize its properties during meiosis and other specialized cellular processes. It is likely that metazoans have evolved a wide range of mechanisms to modify their nuclear envelopes to meet the special demands of meiotic prophase.Homologous chromosome pairing remains one of the most mysterious aspects of meiosis. This new work in mice [1] adds an important piece of the puzzle by illuminating how the nuclear lamina can be modified to facilitate meiotic chromosome dynamics. To understand this process will clearly require looking beyond the chromosomes, and even beyond the nucleus, to the cellular networks connected by LINC complexes.     

Functional redundancy of two C. elegans homologs of the histone chaperone Asf1 in germline DNA replication

Eukaryotic genomes contain either one or two genes encoding homologs of the highly conserved histone chaperone Asf1, however, little is known of their in vivo roles in animal development. UNC-85 is one of the two Caenorhabditis elegans Asf1 homologs and functions in post-embryonic replication in neuroblasts. Although UNC-85 is broadly expressed in replicating cells, the specificity of the mutant phenotype suggested possible redundancy with the second C. elegans Asf1 homolog, ASFL-1. The asfl-1 mRNA is expressed in the meiotic region of the germline, and mutants in either Asf1 genes have reduced brood sizes and low penetrance defects in gametogenesis. The asfl-1, unc-85 double mutants are sterile, displaying defects in oogenesis and spermatogenesis, and analysis of DNA synthesis revealed that DNA replication in the germline is blocked. Analysis of somatic phenotypes previously observed in unc-85 mutants revealed that they are neither observed in asfl-1 mutants, nor enhanced in the double mutants, with the exception of enhanced male tail abnormalities in the double mutants. These results suggest that the two Asf1 homologs have partially overlapping functions in the germline, while UNC-85 is primarily responsible for several Asf1 functions in somatic cells, and is more generally involved in replication throughout development.