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Orthology function

Anastasia K Atabekova, Anna V Pankratenko, Svetlana S Makarova, Ekaterina A Lazareva, Robert A Owens, Andrey G Solovyev, Sergey Y Morozov
Human B-cell receptor-associated protein BAP31 (HsBAP31) is the endoplasmic reticulum-resident protein involved in protein sorting and transport as well as pro-apoptotic signaling. Plant orthologs of HsBAP31 termed 'plant BAP-like proteins' (PBL proteins) have thus far remained unstudied. Recently, the PBL protein from Nicotiana tabacum (NtPBL) was identified as an interactor of Nt-4/1, a plant protein known to interact with plant virus movement proteins and affect the long-distance transport of potato spindle tuber viroid (PSTVd) via the phloem...
October 19, 2016: Biochimie
Sangmi Oh, Ichiro Kawasaki, Jae-Hyung Park, Yhong-Hee Shim
Cell division cycle 25 (cdc25) is an evolutionarily conserved phosphatase that promotes cell cycle progression. Among the four cdc25 orthologs in Caenorhabditis elegans, we found that cdc-25.4 mutant males failed to produce outcrossed progeny. This was not caused by defects in sperm development, but by defects in male mating behavior. The cdc-25.4 mutant males showed various defects during male mating, including contact response, backing, turning, and vulva location. Aberrant turning behavior was the most prominent defect in the cdc-25...
October 21, 2016: G3: Genes—Genomes—Genetics
Evgeny Z Kvon, Olga K Kamneva, Uirá S Melo, Iros Barozzi, Marco Osterwalder, Brandon J Mannion, Virginie Tissières, Catherine S Pickle, Ingrid Plajzer-Frick, Elizabeth A Lee, Momoe Kato, Tyler H Garvin, Jennifer A Akiyama, Veena Afzal, Javier Lopez-Rios, Edward M Rubin, Diane E Dickel, Len A Pennacchio, Axel Visel
The evolution of body shape is thought to be tightly coupled to changes in regulatory sequences, but specific molecular events associated with major morphological transitions in vertebrates have remained elusive. We identified snake-specific sequence changes within an otherwise highly conserved long-range limb enhancer of Sonic hedgehog (Shh). Transgenic mouse reporter assays revealed that the in vivo activity pattern of the enhancer is conserved across a wide range of vertebrates, including fish, but not in snakes...
October 20, 2016: Cell
Brody Holohan, Wanil Kim, Tsung-Po Lai, Hirotoshi Hoshiyama, Ning Zhang, Anas M Alazami, Woodring E Wright, M Stephen Meyn, Fowzan S Alkuraya, Jerry W Shay
BACKGROUND: Loss of function in genes required for telomere maintenance result in disorders known as telomeropathies, which are characterized by a pattern of symptoms including generalized and specific lymphocytopenias as well as very short telomere length and disease anticipation. METHODS: Because human LARP7 is the most likely ortholog of the Tetrahymena p65 protein, which is required for telomerase activity in that organism, we investigated the effects of LARP7 silencing in human cells as well as in two distinct families with Alazami syndrome (loss of function of LARP7)...
October 17, 2016: BMC Genomics
Hyundoo Jeong, Xiaoning Qian, Byung-Jun Yoon
BACKGROUND: Comparative analysis of protein-protein interaction (PPI) networks provides an effective means of detecting conserved functional network modules across different species. Such modules typically consist of orthologous proteins with conserved interactions, which can be exploited to computationally predict the modules through network comparison. RESULTS: In this work, we propose a novel probabilistic framework for comparing PPI networks and effectively predicting the correspondence between proteins, represented as network nodes, that belong to conserved functional modules across the given PPI networks...
October 6, 2016: BMC Bioinformatics
Ayush Attery, Janendra K Batra
Ribonuclease A family is a group of proteins having similar structures and catalytic mechanism but different functions. Human eosinophil granules contain two ribonucleases belonging to the RNase A family, eosinophil cationic protein (ECP) and eosinophil derived neurotoxin (EDN). In mouse, 15 orthologs of EDN and ECP, called mouse eosinophil associated ribonucleases (mEARs) have been reported which are expressed under different pathophysiological conditions. In this study, we have characterized mEAR2, mEAR5, mEAR7 and mEAR11, and compared them with ECP for their catalytic, cytotoxic, antibacterial and antiparasitic activities...
October 17, 2016: International Journal of Biological Macromolecules
Chao-Jun Lu, Bao-Yu Tian, Yi Cao, Cheng-Gang Zou, Ke-Qin Zhang
Nuclear receptors (NRs) are a diverse class of transcription factors, which are involved in regulating a large number of physiological events in metazoans. However, the function of NRs is poorly understood in plant-parasitic nematodes. Here, members of the NR1J+K group of NRs in nematodes, including the free-living and plant parasites, were examined and phylogenetically analyzed. We found that the number of members of the NR1J+K group in plant-parasitic nematodes was less than that in the free-living nematodes, suggesting this reduction of NR1J+K group members in plant parasites maybe arose during the separation of the free-living and intermediately plant parasitic nematodes (Bursaphelenchus xylophilus)...
October 20, 2016: Scientific Reports
Zhongzhen Wu, Jintian Lin, He Zhang, Xinnian Zeng
The oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae), is one of the most destructive pests throughout tropical and subtropical regions in Asia. This insect displays remarkable changes during different developmental phases in olfactory behavior between sexually immature and mated adults. The olfactory behavioral changes provide clues to examine physiological and molecular bases of olfactory perception in this insect. We comparatively analyzed behavioral and neuronal responses of B. dorsalis adults to attractant semiochemicals, and the expression profiles of antenna chemosensory genes...
2016: Frontiers in Physiology
Dekai Wang, Heqin Liu, Guowei Zhai, Liangsheng Wang, Jianfeng Shao, Yuezhi Tao
Functional chloroplast generation depends on the precise coordination of gene expression between the plastid and the nucleus and is essential for plant growth and development. In this study, a rice (Oryza sativa) mutant that exhibited albino and seedling-lethal phenotypes was isolated from a(60)Co-irradiated rice population. The mutant gene was identified as an ortholog of the Arabidopsis plastid transcriptionally active chromosome protein 2 (pTAC2) gene, and the mutant strain was designated osptac2. Sequence and transcription analyses showed that OspTAC2 encodes a putative chloroplast protein consisting of 10 pentratricopeptide repeat (PPR) domains and a C-terminal small MutS-related (SMR) domain...
September 15, 2016: Journal of Genetics and Genomics, Yi Chuan Xue Bao
Awa Diop, Saber Khelaifia, Nicholas Armstrong, Noémie Labas, Pierre-Edouard Fournier, Didier Raoult, Matthieu Million
BACKGROUND: Microbial culturomics represents an ongoing revolution in the characterization of environmental and human microbiome. METHODS: By using three media containing high salt concentration (100, 150, and 200 g/L), the halophilic microbial culturome of a commercial table salt was determined. RESULTS: Eighteen species belonging to the Terrabacteria group were isolated including eight moderate halophilic and 10 halotolerant bacteria. Gracilibacillus massiliensis sp...
2016: Microbial Ecology in Health and Disease
Daifeng Wang, Fei He, Sergei Maslov, Mark Gerstein
Gene expression is controlled by the combinatorial effects of regulatory factors from different biological subsystems such as general transcription factors (TFs), cellular growth factors and microRNAs. A subsystem's gene expression may be controlled by its internal regulatory factors, exclusively, or by external subsystems, or by both. It is thus useful to distinguish the degree to which a subsystem is regulated internally or externally-e.g., how non-conserved, species-specific TFs affect the expression of conserved, cross-species genes during evolution...
October 2016: PLoS Computational Biology
Graeme Milligan, Daniele Bolognini, Eugenia Sergeev
A large number of reviews and commentaries have highlighted the potential role of the short-chain fatty acid receptors GPR41 (FFA3) and, particularly, GPR43 (FFA2) as an interface between the intestinal microbiota and metabolic and inflammatory disorders. However, short-chain fatty acids have very modest potency and display limited selectivity between these two receptors, and studies on receptor knockout mice have resulted in non-uniform conclusions; therefore, selective and high-potency/high-affinity synthetic ligands are required to further explore the contribution of these receptors to health and disease...
October 19, 2016: Handbook of Experimental Pharmacology
Junting Pan, Weidong Wang, Dongqin Li, Zaifa Shu, Xiaoli Ye, Pinpin Chang, Yuhua Wang
BACKGROUND: Nitric oxide (NO) functions as a critical signaling molecule in the low-temperature stress responses in plants, including polarized pollen tube growth in Camellia sinensis. Despite this, the potential mechanisms underlying the participation of NO in pollen tube responses to low temperature remain unclear. Here, we investigate alterations to gene expression in C. sinensis pollen tubes exposed to low-temperature stress and NO using RNA-Seq technology, in order to find the potential candidate genes related to the regulation of pollen tube elongation by NO under low-temperature stress...
October 18, 2016: BMC Genomics
Zhaojun Cao, Yue Yin, Xuan Sun, Jun Han, Qing Peng Sun, Min Lu, Jinbao Pan, Weixiang Wang
Ash1 is a known H3K36-specific histone demethylase that is required for normal Hox gene expression and fertility in Drosophila and mammals. However, little is known about the expression and function of the fungal ortholog of Ash1 in phytopathogenic fungus Magnaporthe oryzae. Here we report that MoKMT2H, an Ash1-like protein, is required for conidium germination and virulence in rice. We obtained MoKMT2H null mutant (ΔMoKMT2H) using a target gene replacement strategy. In the ΔMoKMT2H null mutants, global histone methyltransferase modifications (H3K4me3, H3K9me3, H3K27me3, and H3K36me2/3) of the genome were unaffected...
2016: BioMed Research International
Zhu Chen, Danmei Chen, Wenyuan Chu, Dongyue Zhu, Hanwei Yan, Yan Xiang
Whole-genome duplication events have occurred more than once in the genomes of some rosids and played a significant role over evolutionary time. Lipoxygenases (LOXs) are involved in many developmental and resistance processes in plants. Our study concerns the subject of the LOX gene family; we tracked the evolutionary process of ancestral LOX genes in four modern rosids. Here we show that some members of the LOX gene family in the Arabidopsis genome are likely to be lost during evolution, leading to a smaller size than that in Populus, Vitis, and Carica...
2016: Frontiers in Genetics
Akinori Suzuki, Hidero Komata, Shogo Iwashita, Shotaro Seto, Hironobu Ikeya, Mitsutoshi Tabata, Takashi Kitano
In vertebrates, there are four major genes in the RH (Rhesus) gene family, RH, RHAG, RHBG, and RHCG. These genes are thought to have been formed by the two rounds of whole-genome duplication (2R-WGD) in the common ancestor of all vertebrates. In our previous work, where we analyzed details of the gene duplications process of this gene family, three nucleotide sequences belonging to this family were identified in Far Eastern brook lamprey (Lethenteron reissneri), and the phylogenetic positions of the genes were determined...
October 13, 2016: Molecular Phylogenetics and Evolution
Yanli Xiang, Xiaopeng Sun, Shan Gao, Feng Qin, Mingqiu Dai
Drought is a major abiotic stress that causes the yearly yield loss of maize, a crop cultured worldwide, thus breeding drought tolerant maize cultivars is a priority target of the world agriculture. Clade A PP2C phosphatases (PP2C-A) are conserved in plants and are important for ABA signaling and plant drought response. However, the natural variations of PP2C-A genes that directly associated with levels of drought tolerance remain to be elucidated. Here, we conducted a candidate gene association analysis of ZmPP2C-A gene family in a maize panel consisting of 368 varieties collected worldwide, and identified a drought responsive gene ZmPP2C-A10 that is tightly associated with drought tolerance...
October 13, 2016: Molecular Plant
Lianshuo Li, Zicheng Wang, Peng He, Shining Ma, Jie Du, Rui Jiang
Although networks of microbial species have been widely used in the analysis of 16S rRNA sequencing data of a microbiome, the construction and analysis of a complete microbial gene network is in general problematic because of the large number of microbial genes in metagenomics studies. To overcome this limitation, we propose to map microbial genes to functional units, including KEGG orthologous groups and the evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) orthologous groups, to enable the construction and analysis of a microbial functional network...
October 13, 2016: Genomics, Proteomics & Bioinformatics
Teija Ojala, Pia K S Laine, Terhi Ahlroos, Jarna Tanskanen, Saara Pitkänen, Tuomas Salusjärvi, Matti Kankainen, Soile Tynkkynen, Lars Paulin, Petri Auvinen
Propionibacterium freudenreichii is a commercially important bacterium that is essential for the development of the characteristic eyes and flavor of Swiss-type cheeses. These bacteria grow actively and produce large quantities of flavor compounds during cheese ripening at warm temperatures but also appear to contribute to the aroma development during the subsequent cold storage of cheese. Here, we advance our understanding of the role of P. freudenreichii in cheese ripening by presenting the 2.68-Mbp annotated genome sequence of P...
September 26, 2016: International Journal of Food Microbiology
Rinki Murphy, Peter Tsai, Mia Jüllig, Amy Liu, Lindsay Plank, Michael Booth
BACKGROUND: It is unclear whether specific gut microbiota is associated with remission of type 2 diabetes (T2D) after distinct types of bariatric surgery. AIMS: The aim of this study is to examine gut microbiota changes after laparoscopic Roux-en-Y gastric bypass (RYGB) or sleeve gastrectomy (SG) surgery in obese patients with T2D. METHODS: Whole-metagenome shotgun sequencing of DNA fragments using Illumina HiSeq2000 was obtained from stool samples collected from 14 obese T2D patients pre-operatively (while on very low calorie diet) and 1 year after randomisation to laparoscopic SG (n = 7) or RYGB (n = 7)...
October 13, 2016: Obesity Surgery
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