Mycoplasma CG- and GATC-specific DNA methyltransferases selectively and efficiently methylate the host genome and alter the epigenetic landscape in human cells

Aberrant DNA methylation is frequently observed in disease, including many cancer types, yet the underlying mechanisms remain unclear. Because germline and somatic mutations in the genes that are responsible for DNA methylation are infrequent in malignancies, additional mechanisms must be considered. Mycoplasmas spp., including Mycoplasma hyorhinis, efficiently colonize human cells and may serve as a vehicle for delivery of enzymatically active microbial proteins into the intracellular milieu. Here, we performed, for the first time, genome-wide and individual gene mapping of methylation marks generated by the M. hyorhinis CG- and GATC-specific DNA cytosine methyltransferases (MTases) in human cells. Our results demonstrated that, upon expression in human cells, MTases readily translocated to the cell nucleus. In the nucleus, MTases selectively and efficiently methylated the host genome at the DNA sequence sites free from pre-existing endogenous methylation, including those in a variety of cancer-associated genes. We also established that mycoplasma is widespread in colorectal cancers, suggesting that either the infection contributed to malignancy onset or, alternatively, that tumors provide a favorable environment for mycoplasma growth. In the human genome, ∼11% of GATC sites overlap with CGs (e.g., CGAT^mCG); therefore, the methylated status of these sites can be perpetuated by human DNMT1. Based on these results, we now suggest that the GATC-specific methylation represents a novel type of infection-specific epigenetic mark that originates in human cells with a previous exposure to infection. Overall, our findings unveil an entirely new panorama of interactions between the human microbiome and epigenome with a potential impact in disease etiology.     

Evolutionary walk between (β/α)(8) barrels: catalytic migration from triosephosphate isomerase to thiamin phosphate synthase

The functionally versatile (β/α)(8) barrel scaffold was used to migrate triosephosphate isomerase (TPI) to thiamin phosphate synthase (TPS) activity, two enzymes that share the same fold but catalyze unrelated reactions through different mechanisms. The high sensitivity of the selection methodology was determinant to succeed in finding proteins with the desired activity. A combination of rational design and random mutagenesis was used to achieve the desired catalytic migration. One of the parallel directed evolution strategies followed resulted in TPI derivatives able to complement the thiamin phosphate auxotrophy phenotype of an Escherichia coli strain deleted of thiE, the gene that codes for TPS. Successive rounds of directed evolution resulted in better complementing TPI variants. Biochemical characterization of some of the evolved TPI clones demonstrated that the K(m) for the TPS substrates was similar to that of the native TPS; however and in agreement with the very slow complementation phenotype, the k(cat) was 4 orders of magnitude lower, indicating that substrate binding played a major role on selection. Interestingly, the crystal structure of the most proficient variant showed a slightly modified TPI active site occupied by a thiamin-phosphate-like molecule. Substitution of key residues in this region reduced TPS activity, strongly suggesting that this is also the catalytic site for the evolved TPS activity. The presence of the TPS reaction product at the active site explains the fast inactivation of the enzyme observed. In conclusion, by combining rational design, random mutagenesis and a very sensitive selection, it is possible to achieve enzymatic activity migration.     

Heavy chains of inter alpha inhibitor (IαI) inhibit the human complement system at early stages of the cascade

Inter alpha inhibitor (IαI) is an abundant serum protein consisting of three polypeptides: two heavy chains (HC1 and HC2) and bikunin, a broad-specificity Kunitz-type proteinase inhibitor. The complex is covalently held together by chondroitin sulfate but during inflammation IαI may interact with TNF-stimulated gene 6 protein (TSG-6), which supports transesterification of heavy chains to hyaluronan. Recently, IαI was shown to inhibit mouse complement in vivo and to protect from complement-mediated lung injury but the mechanism of such activity was not elucidated. Using human serum depleted from IαI, we found that IαI is not an essential human complement inhibitor as was reported for mice and that such serum has unaltered hemolytic activity. However, purified human IαI inhibited classical, lectin and alternative complement pathways in vitro when added in excess to human serum. The inhibitory activity was dependent on heavy chains but not bikunin and detected at the level of initiating molecules (MBL, properdin) in the lectin/alternative pathways or C4b in the classical pathway. Furthermore, IαI affected formation and assembly of the C1 complex and prevented assembly of the classical pathway C3-convertase. Presence and putative interactions with TSG-6 did not affect the ability of IαI to inhibit complement thus implicating IαI as a potentially important complement inhibitor once enriched onto hyaluronan moieties in the course of local inflammatory processes. In support of this, we found a correlation between IαI/HC-containing proteins and hemolytic activity of synovial fluid from patients suffering from rheumatoid arthritis.     

Current status and perspectives of plant-based candidate vaccines against the human immunodeficiency virus (HIV)

Genetically engineered plants are economical platforms for the large-scale production of recombinant proteins and have been used over the last 21 years as models for oral vaccines against a wide variety of human infectious and autoimmune diseases with promising results. The main inherent advantages of this approach consist in the absence of purification needs and easy production and administration. One relevant infectious agent is the human immunodeficiency virus (HIV), since AIDS evolved as an alarming public health problem implicating very high costs for government agencies in most African and developing countries. The design of an effective and inexpensive vaccine able to limit viral spread and neutralizing the viral entry is urgently needed. Due to the limited efficacy of the vaccines assessed in clinical trials, new HIV vaccines able to generate broad immune profiles are a priority in the field. This review discusses the current advances on the topic of using plants as alternative expression systems to produce functional vaccine components against HIV, including antigens from Env, Gag and early proteins such as Tat and Nef. Ongoing projects of our group based on the expression of chimeric proteins comprising C4 and V3 domains from gp120, as an approach to elicit broadly neutralizing antibodies are mentioned. The perspectives of the revised approaches, such as the great need of assessing the oral immunogenicity and a detailed immunological characterization of the elicited immune responses, are also discussed.     

Distributional patterns of freshwater taxa (fishes, crustaceans and plants) from the Mexican Transition Zone

Aim  To test whether distributional patterns of Neotropical freshwater taxa fit the generalized tracks already postulated for terrestrial groups occurring in the Mexican Transition Zone.
Location  The study units comprised 17 hydrological basins located along the Pacific coast of the Americas from Mexico to Panama, and in the Gulf of Mexico from the Papaloapan to the Grijalva–Usumacinta basin.
Methods  Distributional data for 22 fish species, 34 crab species of the tribe Pseudothelphusini, and 22 strictly freshwater species of angiosperms were analysed. Parsimony analysis of endemicity is based on presence/absence data of these taxa and uses the computer programs Winclada and NONA.
Results  Three generalized tracks were obtained: (1) Mexican North Pacific, (2) Mexican Central Pacific, and (3) Southern Mexico–Guatemala. A node resulted at the intersection of the first two tracks, coinciding with the Neovolcanic Axis in central Mexico.
Main conclusions  Freshwater generalized tracks with an altitudinal distribution below 1000 m, mainly including fishes and angiosperms, are close to the Tropical Mesoamerican generalized track. Generalized tracks above 1000 m, including freshwater crabs, have a stronger affinity with the Mountain Mesoamerican track. The Isthmus of Tehuantepec represents a node for the Neotropical freshwater and terrestrial biota. These results seem to indicate that common geobiotic processes have induced these patterns.     

FBXO25, an F-box protein homologue of atrogin-1, is not induced in atrophying muscle

Atrogin-1/MAFbx/FBXO32 is a muscle-specific ubiquitin-ligase (E3) that is dramatically increased in atrophying muscle. Here, we have investigated the functional relationship between atrogin-1 and FBXO25 which shares 65% amino acid identity. Using a RT-PCR, we demonstrated that FBXO25 is highly expressed in brain, kidney, and intestine, whereas atrogin-1 expression is largely restricted to striate muscle. FBXO25 was shown here to contain a functional F-box domain that binds to Skp1 and thereby to Roc1 and Cul1, the major components of SCF-type E3s. In addition, the productive SCF complex containing FBXO25 showed ubiquitin ligase activity. We investigated the differential expression of atrogin-1 and FBXO25 in fasted and dexamethasone-treated mice and also in rats with streptozotocin-induced diabetes. Although the atrogin-1 was strongly induced in muscle in all three models, no changes were observed in the expression of FBXO25. Therefore, here we have shown that FBXO25 is a novel F-box protein analogous to atrogin-1, which is not involved in muscle atrophy. Further functional studies should elucidate the exact role of FBXO25 in the ubiquitin-proteasome pathway.     

Interaction analysis of the AAA ATPase TAA43 by the bacterial two-hybrid system

The TAA43 ATPase of Thermoplasma acidophilum, an archaeal member of the AAA protein family, is known to have an atypical oligomeric state and a nonspecific association with high-molecular-weight protein complexes. We assessed the in vivo binding pattern of TAA43 using the bacterial two-hybrid system. We found 36 positive isolates interacting with TAA43. Our analysis showed that TAA43 interacts preferentially with nonribosomal proteins containing ribosomal domains and regions involved in RNA metabolism.