Biophysics and Structure-Function Relationships of LRRC8-Formed Volume-Regulated Anion Channels

Volume-regulated anion channels (VRACs) are key players in regulatory volume decrease of vertebrate cells by mediating the extrusion of chloride and organic osmolytes. They play additional roles in various physiological processes beyond their role in osmotic volume regulation. VRACs are formed by heteromers of LRRC8 proteins; LRRC8A (also called SWELL1) is an essential subunit that combines with any of its paralogs, LRRC8B–E, to form hexameric VRAC complexes. The subunit composition of VRACs determines electrophysiological characteristics of their anion transport such as single-channel conductance, outward rectification, and depolarization-dependent inactivation kinetics. In addition, differently composed VRACs conduct diverse substrates, such as LRRC8D enhancing VRAC permeability to organic substances like taurine or cisplatin. Here, after a recapitulation of the biophysical properties of VRAC-mediated ion and osmolyte transport, we summarize the insights gathered since the molecular identification of VRACs. We describe the recently solved structures of LRRC8 complexes and discuss them in terms of their structure-function relationships. These studies open up many potential avenues for future research.     

Regulators of cell volume: The structural and functional properties of anion channels of the LRRC8 family

Members of the LRRC8 family participate in the response of vertebrate cells to osmotic changes in their environment. These proteins form heteromeric assemblies composed of the obligatory subunit LRRC8A and at least one of the other four homologs, which together function as anion-selective channels with distinct properties that are activated upon cell-swelling. The hexameric complexes share a conserved architecture consisting of a membrane-inserted pore domain with an ion permeation path located at the axis of symmetry and cytoplasmic leucine-rich repeat domains that regulate the open probability of the channel. In this review, we summarize the current understanding of structure–function relationships of these unusual ion channels whose mechanisms are, despite their large physiological importance, still poorly understood.     

LRRC8 involved in B cell development belongs to a novel family of leucine-rich repeat proteins

In a previous study, we isolated a novel gene, LRRC8 (leucine-rich repeat-containing 8), in a girl with congenital agammaglobulinemia. We have now identified four unknown LRRC8-like genes, named TA-LRRP, AD158, LRRC5, and FLJ23420. Their predicted structures are very similar to each other, and highly conserved between humans and the mouse. All five genes encode proteins consisting of 16 extracellular leucine-rich repeats (LRRs), all of which have four transmembrane regions except for FLJ23420. These genes belong to a novel family, designated the LRRC8 family, within the superfamily of LRR proteins. TA-LRRP, AD158, and LRRC5 might be implicated in proliferation and activation of lymphocytes and monocytes.     

LRRC4通过LRR结构域抑制脑胶质母细胞瘤U251细胞的生长和侵袭

LRRC4基因是候选的脑胶质瘤抑制基因,其细胞外区域含有一个保守的LRR和一个IgC2 结构域.本研究结合生物信息学分析,通过一步PCR法构建了不同结构域缺失的突变体（pc ΔLRR, pcΔIgC2或pcΔTm）.并将全长LRRC4（pcLRRC4）和各突变体转染至U251细胞,构建了稳定表达的U251细胞系.通过MTT,软琼脂集落形成及Transwell体外侵袭模型检测发现,全长LRRC4能够抑制U251细胞的生长和侵袭;LRR结构域缺失的突变体不再抑制U251细胞的生长和侵袭;而IgC2或Tm区缺失的突变体仍然可以抑制U251细胞的生长和侵袭.该结果表明,LRRC4抑制U251细胞的生长和侵袭依赖于它的LRR结构域,而不是IgC2或Tm结构域.     

Loss-of-Function Mutations in LRRC6, a Gene Essential for Proper Axonemal Assembly of Inner and Outer Dynein Arms,Cause Primary Ciliary Dyskinesia

Primary ciliary dyskinesia (PCD) is a group of autosomal-recessive disorders resulting from cilia and sperm-flagella defects, which lead to respiratory infections and male infertility. Most implicated genes encode structural proteins that participate in the composition of axonemal components, such as dynein arms (DAs), that are essential for ciliary and flagellar movements; they explain the pathology in fewer than half of the affected individuals. We undertook this study to further understand the pathogenesis of PCD due to the absence of both DAs. We identified, via homozygosity mapping, an early frameshift in LRRC6, a gene that encodes a leucine-rich-repeat (LRR)-containing protein. Subsequent analyses of this gene mainly expressed in testis and respiratory cells identified biallelic mutations in several independent individuals. The situs inversus observed in two of them supports a key role for LRRC6 in embryonic nodal cilia. Study of native LRRC6 in airway epithelial cells revealed that it localizes to the cytoplasm and within cilia, whereas it is absent from cells with loss-of-function mutations, in which DA protein markers are also missing. These results are consistent with the transmission-electron-microscopy data showing the absence of both DAs in cilia or flagella from individuals with LRRC6 mutations. In spite of structural and functional similarities between LRRC6 and DNAAF1, another LRR-containing protein involved in the same PCD phenotype, the two proteins are not redundant. The evolutionarily conserved LRRC6, therefore, emerges as an additional player in DA assembly, a process that is essential for proper axoneme building and that appears to be much more complex than was previously thought.     

The leucine-rich repeat domains of BK channel auxiliary γ subunits regulate their expression,trafficking, and channel-modulation functions

As high-conductance calcium- and voltage-dependent potassium channels, BK channels consist of pore-forming, voltage-, and Ca²⁺-sensing α and auxiliary subunits. The leucine-rich repeat (LRR) domain–containing auxiliary γ subunits potently modulate the voltage dependence of BK channel activation. Despite their dominant size in whole protein masses, the function of the LRR domain in BK channel γ subunits is unknown. We here investigated the function of these LRR domains in BK channel modulation by the auxiliary γ1–3 (LRRC26, LRRC52, and LRRC55) subunits. Using cell surface protein immunoprecipitation, we validated the predicted extracellular localization of the LRR domains. We then refined the structural models of mature proteins on the membrane via molecular dynamic simulations. By replacement of the LRR domain with extracellular regions or domains of non-LRR proteins, we found that the LRR domain is nonessential for the maximal channel-gating modulatory effect but is necessary for the all-or-none phenomenon of BK channel modulation by the γ1 subunit. Mutational and enzymatic blockade of N-glycosylation in the γ1–3 subunits resulted in a reduction or loss of BK channel modulation by γ subunits. Finally, by analyzing their expression in whole cells and on the plasma membrane, we found that blockade of N-glycosylation drastically reduced total expression of the γ2 subunit and the cell surface expression of the γ1 and γ3 subunits. We conclude that the LRR domains play key roles in the regulation of the expression, cell surface trafficking, and channel-modulation functions of the BK channel γ subunits.     

The Protein Synthesis Inhibitor Blasticidin S Enters Mammalian Cells via Leucine-rich Repeat-containing Protein 8D

Leucine-rich repeat-containing 8 (LRRC8) proteins have been identified as putative receptors involved in lymphocyte development and adipocyte differentiation. They remain poorly characterized, and no specific function has been assigned to them. There is no consensus on how this family of proteins might function because homology searches suggest that members of the LRRC8 family act not as plasma membrane receptors, but rather as channels that mediate cell-cell signaling. Here we provide experimental evidence that supports a role for LRRC8s in the transport of small molecules. We show that LRRC8D is a mammalian protein required for the import of the antibiotic blasticidin S. We characterize localization and topology of LRRC8A and LRRC8D and demonstrate that LRRC8D interacts with LRRC8A, LRRC8B, and LRRC8C. Given the suggested involvement in solute transport, our results support a model in which LRRC8s form one or more complexes that may mediate cell-cell communication by transporting small solutes.     

Subunit composition of VRAC channels determines substrate specificity and cellular resistance to Pt‐based anti‐cancer drugs

Although platinum‐based drugs are widely used chemotherapeutics for cancer treatment, the determinants of tumor cell responsiveness remain poorly understood. We show that the loss of subunits LRRC8A and LRRC8D of the heteromeric LRRC8 volume‐regulated anion channels (VRACs) increased resistance to clinically relevant cisplatin/carboplatin concentrations. Under isotonic conditions, about 50% of cisplatin uptake depended on LRRC8A and LRRC8D, but neither on LRRC8C nor on LRRC8E. Cell swelling strongly enhanced LRRC8‐dependent cisplatin uptake, bolstering the notion that cisplatin enters cells through VRAC. LRRC8A disruption also suppressed drug‐induced apoptosis independently from drug uptake, possibly by impairing VRAC‐dependent apoptotic cell volume decrease. Hence, by mediating cisplatin uptake and facilitating apoptosis, VRAC plays a dual role in the cellular drug response. Incorporation of the LRRC8D subunit into VRAC substantially increased its permeability for cisplatin and the cellular osmolyte taurine, indicating that LRRC8 proteins form the channel pore. Our work suggests that LRRC8D‐containing VRACs are crucial for cell volume regulation by an important organic osmolyte and may influence cisplatin/carboplatin responsiveness of tumors.     

Leucine-rich repeat C4 protein is involved in nervous tissue development and neurite outgrowth, and induction of glioma cell differentiation

LRRC4, leucine-rich repeat C4 protein, has been identified in human （GenBank accession No. AF196976）, mouse （GenBank accession No. DQ177325）, rat （GenBank accession No. DQ119102） and bovine （GenBank accession No. DQ 164537） with identical domains. In terms of their similarity, the genes encoding LRRC4 in these four mammalian species are orthogs and therefore correspond to the same gene entity. Based on previous research, and using in situ hybridization, we found that LRRC4 had the strongest expression in hippocampal CA1 and CA2, the granule cells of the dentate gyrus region, the mediodoral thalamic nucleus, and cerebella Purkinje cell layers. Using a P19 cell model, we also found that LRRC4 participates in the differentiation of neuron and glia cells. In addition, extracellular proteins containing both an LRR cassette and immunoglobulin domains have been shown to participate in axon guidance. Our data from neurite outgrowth assays indicated that LRRC4 promoted neurite extension of hippocampal neurons, and induced differentiation of glioblastoma U251 cells into astrocyte-like cells, confirmed by morphology observation and glial fibrillary acidic protein expression.     

Expression and functional characterization of LRRC4, a novel brain-specific member of the LRR superfamily

LRRC4, a novel member of LRR superfamily thought to be involved in development and tumorigenesis of the nervous tissue, has the potential to suppress tumorigenesis and cell proliferation of U251MG cells. This study aimed at revealing the correlation between expression of LRRC4 and the maintenance of normal function and tumorigenesis suppression within the central nervous system. We systematically analyzed the expression and tissue distributions of the gene in tissues. Results showed that LRRC4 expression was limited to normal adult brain, both in human and in mouse, and exhibited a development-regulated pattern, but was down-regulated in brain tumor tissues and U251MG cell line. Furthermore, dynamic alterations in gene expression associated with cell cycle progression were investigated by using Tet-on system. Results showed that LRRC4 induced a cell cycle delay at the late G1 phase, probably through the alteration of the expression of different cell cycle regulating proteins responsible for mediating G1-S progression, such as p21(Waf1/Cip1) and p27(Kip1), Cdk2 and PCNA, p-ERK1/2. These findings suggest that LRRC4 may play an important role in maintaining normal function and suppressing tumorigenesis in the central nervous system.     

Leucine‐rich repeat receptor‐like kinase II phylogenetics reveals five main clades throughout the plant kingdom

Receptor‐like kinases (RLKs) represent the largest group of cell surface receptors in plants. The monophyletic leucine‐rich repeat (LRR)‐RLK subfamily II is considered to contain the somatic embryogenesis receptor kinases (SERKs) and NSP‐interacting kinases known to be involved in developmental processes and cellular immunity in plants. There are only a few published studies on the phylogenetics of LRR‐RLKII; unfortunately these suffer from poor taxon/gene sampling. Hence, it is not clear how many and what main clades this family contains, let alone what structure–function relationships exist. We used 1342 protein sequences annotated as ‘SERK’ and ‘SERK‐like’ plus related sequences in order to estimate phylogeny within the LRR‐RLKII clade, using the nematode protein kinase Pelle as an outgroup. We reconstruct five main clades (LRR‐RLKII 1–5), in each of which the main pattern of land plant relationships re‐occurs, confirming previous hypotheses that duplication events happened in this gene subfamily prior to divergence among land plant lineages. We show that domain structures and intron–exon boundaries within the five clades are well conserved in evolution. Furthermore, phylogenetic patterns based on the separate LRR and kinase parts of LRR‐RLKs are incongruent: whereas the LRR part supports a LRR‐RLKII 2/3 sister group relationship, the kinase part supports clades 1/2. We infer that the kinase part includes few ‘radical’ amino acid changes compared with the LRR part. Finally, our results confirm that amino acids involved in each LRR‐RLKII–receptor complex interaction are located at N‐capping residues, and that the short amino acid motifs of this interaction domain are highly conserved throughout evolution within the five LRR‐RLKII clades.     

LRRC4融合蛋白的构建与表达研究

在前期工作中,采用EST介导的定位候选克隆策略,克隆了一个在脑瘤中表达下调的脑特异表达新基因LRRC4,为进一步研究其结构与功能的关系,构建了含LRRC4基因全长编码区的pGEM-T Easy质粒,在此基础上通过亚克隆构建了LRRC4融合蛋白的绿色荧光蛋白（pEGFP-C1）表达质粒,瞬时转染哺乳动物细胞,结果发现表达的LRRC4融合蛋白定位于活细胞的细胞膜上.同时,构建了LRRC4全长和截短型原核表达pGEX-4T-2质粒,成功而高效地在大肠杆菌BL21 中表达LRRC4融合蛋白.上述工作为制备多抗,深入研究LRRC4基因的功能奠定了基础.     

富亮氨酸重复超家族新成员LRRC4的克隆与在脑瘤中的表达分析

在染色体7q31-32多种肿瘤杂合性丢失（loss of heterozygosity,LOH）高频区,采用表达序列标签（expressed sequence tag,EST）介导的定位候选克隆策略获得了一个定位于人染色体7q31-32的新基因（GenBank 登录号: AF196976）.该基因编码653个氨基酸,蛋白质理论pI/m:6.58/72.7 ku.它包含七个典型的LRR、一个IgC2样结构域.此外,它还包含一个N端信号肽、一个C端跨膜区.其结构特征表明它是富亮氨酸重复（leucine-rich repeat,LRR）超家族的新成员.经过人类基因组命名委员会的同意,将该基因命名为LRRC4.此外,通过序列相似性匹配还获得了定位于小鼠6号染色体的LRRC4的同源基因（GenBank 登录号: AF290542）.RNA印迹和RT-PCR检测发现LRRC4在正常人脑组织相对特异表达,而在多种原发性脑瘤表达明显下调或缺失.综合考虑LRRC4基因的序列特征及表达谱,提示LRRC4基因可能在神经系统中发挥重要作用.     

Structure–function analysis of ZAR1 immune receptor reveals key molecular interactions for activity

NLR (nucleotide‐binding [NB] leucine‐rich repeat [LRR] receptor) proteins are critical for inducing immune responses in response to pathogen proteins, and must be tightly modulated to prevent spurious activation in the absence of a pathogen. The ZAR1 NLR recognizes diverse effector proteins from Pseudomonas syringae, including HopZ1a, and Xanthomonas species. Receptor‐like cytoplasmic kinases (RLCKs) such as ZED1, interact with ZAR1 and provide specificity for different effector proteins, such as HopZ1a. We previously developed a transient expression system in Nicotiana benthamiana that allowed us to demonstrate that ZAR1 function is conserved from the Brassicaceae to the Solanaceae. Here, we combined structural modelling of ZAR1, with molecular and functional assays in our transient system, to show that multiple intramolecular and intermolecular interactions modulate ZAR1 activity. We identified determinants required for the formation of the ZAR^CC oligomer and its activity. Lastly, we characterized intramolecular interactions between ZAR1 subdomains that participate in keeping ZAR1 immune complexes inactive. This work identifies molecular constraints on immune receptor function and activation.     

LRRC19, a novel member of the leucine-rich repeat protein family, activates NF-κB and induces expression of proinflammatory cytokines

We have identified a new functional transmembrane receptor, LRRC19 (leucine-rich repeat containing 19), that belongs to the LRR protein family. LRRC19’s central core has four analogous LRR repeating modules in a juxtaposed array and a casein kinase (CK2) phosphorylation site in the cytoplasmic domain. LRRC19 mRNA was found in the kidney, spleen and intestine of adult mice using both RT-PCR and in situ hybridization. LRRC19 does not contain a cytoplasmic Toll/IL-1 receptor (TIR) domain but was able to activate NF-κB and induce production of proinflammatory cytokines. LRRC19 shares a close evolutionary relationship with multiple Toll-like receptors (TLRs), especially TLR3. Importantly, the TLR3 ligand, as well as other TLR ligands, significantly promoted the expression of proinflammatory cytokines and the activation of NF-κB by LRRC19. Thus, LRRC19 may play an important role in inducing innate immune responses in certain tissues such as the kidney.     

Cisplatin activates volume sensitive LRRC8 channel mediated currents in Xenopus oocytes

LRRC8 proteins have been shown to underlie the ubiquitous volume regulated anion channel (VRAC). VRAC channels are composed of the LRRC8A subunit and at least one among the LRRC8B-E subunits. In addition to their role in volume regulation, LRRC8 proteins have been implicated in the uptake of chemotherapeutic agents. We had found that LRRC8 channels can be conveniently expressed in Xenopus oocytes, a system without endogenous VRAC activity. The fusion with fluorescent proteins yielded constitutive activity for A/C, A/D and A/E heteromers. Here we tested the effect of the anticancer drug cisplatin on LRRC8A-VFP/8E-mCherry and LRRC8A-VFP/8D-mCherry co-expressing oocytes. Incubation with cisplatin dramatically activated currents for both subunit combinations, confirming that VRAC channels provide an uptake pathway for cisplatin and that intracellular cisplatin accumulation strongly activates the channels. Thus, specific activators of LRRC8 proteins might be useful tools to counteract chemotherapeutic drug resistance.     

Structure,function and evolution of the hemerythrin‐like domain superfamily

Hemerythrin‐like proteins have generally been studied for their ability to reversibly bind oxygen through their binuclear nonheme iron centers. However, in recent years, it has become increasingly evident that some members of the hemerythrin‐like superfamily also participate in many other biological processes. For instance, the binuclear nonheme iron site of YtfE, a hemerythrin‐like protein involved in the repair of iron centers in Escherichia coli, catalyzes the reduction of nitric oxide to nitrous oxide, and the human F‐box/LRR‐repeat protein 5, which contains a hemerythrin‐like domain, is involved in intracellular iron homeostasis. Furthermore, structural data on hemerythrin‐like domains from two proteins of unknown function, PF0695 from Pyrococcus furiosus and NMB1532 from Neisseria meningitidis, show that the cation‐binding sites, typical of hemerythrin, can be absent or be occupied by metal ions other than iron. To systematically investigate this functional and structural diversity of the hemerythrin‐like superfamily, we have collected hemerythrin‐like sequences from a database comprising fully sequenced proteomes and generated a cluster map based on their all‐against‐all pairwise sequence similarity. Our results show that the hemerythrin‐like superfamily comprises a large number of protein families which can be classified into three broad groups on the basis of their cation‐coordinating residues: (a) signal‐transduction and oxygen‐carrier hemerythrins (H‐HxxxE‐HxxxH‐HxxxxD); (b) hemerythrin‐like (H‐HxxxE‐H‐HxxxE); and, (c) metazoan F‐box proteins (H‐HExxE‐H‐HxxxE). Interestingly, all but two hemerythrin‐like families exhibit internal sequence and structural symmetry, suggesting that a duplication event may have led to the origin of the hemerythrin domain.     

Profiling of differentially expressed genes in LRRC4 overexpressed glioblastoma cells by cDNA array

Our previous study has shown that LRRC4 is a novel member of the leucine-rich repeat （LRR） superfamily and has the potential to suppress brain tumor growth. In order to further analyze the functions of LRRC4 on the maintenance of normal function and suppression of tumorigenesis in the central nervous system, we investigated alterations in gene expression related to neurobiology by the Atlas array in two inducible dual-stable LRRC4-overexpressing cell lines. Seventeen of 588 genes spotted on the Atlas membrane showed altered expression levels in LRRC4 transfected U251MG Tet-on cells, which are involved in cell proliferation and cell cycle progression, tumor invasion and metastasis, and neurotransmitter synthesis and release. In addition, cell invasion assay results showed that LRRC4 can inhibit the U251MG cell migration. These studies represent the first cDNA array analysis of the effects of LRRC4 on the involvement of different neurobiological genes in U251MG glioblastoma cells and provide new insights into the function of LRRC4 in glioma.     

Analyses of non-leucine-rich repeat (non-LRR) regions intervening between LRRs in proteins

Background

Many proteins have LRR (leucine-rich repeat) units interrupted by non-LRRs which we call IR (non-LRR island region).

Methods

We identified proteins containing LRR@IRs (LRRs having IR) by using a new method and then analyzed their natures and distributions.

Results

LRR@IR proteins were found in over two hundred proteins from prokaryotes and from eukaryotes. These are divided into twenty-one different protein families. The IRs occur one to four times in LRR regions and range in length from 5 to 11,265 residues. The IR lengths in Fungi adenylate cyclases (acys) range from 5 to 116 residues; there are 22 LRR repeats. The IRs in Leishmania proteophosphoglycans (ppgs) vary from 105 to 11,265 residues. These results indicate that the IRs evolved rapidly. A group of LRR@IR proteins—LRRC17, chondroadherin-like protein, ppgs, and four Pseudomonas proteins—have a super motif consisting of an LRR block and its adjacent LRR@IR region. This indicates that the entire super motif experienced duplication. The sequence analysis of IRs offers functional similarity in some LRR@IR protein families.

General significance

This study suggests that various IRs and super motifs provide a great variety of structures and functions for LRRs.