GH101 FAMILY OF GLYCOSIDE HYDROLASES: SUBFAMILY STRUCTURE AND EVOLUTIONARY CONNECTIONS WITH OTHER FAMILIES

2010 ◽  
Vol 08 (03) ◽  
pp. 437-451 ◽  
Author(s):  
DANIIL G. NAUMOFF
Keyword(s):  
Sequence Comparison ◽  
Catalytic Domain ◽  
Evolutionary Relationship ◽  
Glycoside Hydrolases ◽  
Pairwise Sequence Comparison ◽  
Homologous Proteins ◽  
Protein Database ◽  
Domain Structures ◽  
The Family ◽  
Relationship Of

The GH101 family is composed of endo-α-N-acetylgalactosaminidases and their homologues. Pairwise sequence comparison and phylogenetic analysis allowed us to distinguish five to six subfamilies in this family. Diverse domain structures were found among the family members. Usually they have five irreplaceable and some optional domains. Iterative screening of the protein database revealed an evolutionary relationship of the GH101 catalytic domain with glycoside hydrolase domains from GH13, GH31, and GH70 families. Among other homologous proteins we have found representatives of COG1649, as well as members of four new families of predicted glycoside hydrolases (GHL1-GHL4).

scholarly journals Comparison of viromes in vaginal secretion from pregnant women with and without vaginitis

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
He-Teng Zhang ◽  
Hao Wang ◽  
Hai-Sheng Wu ◽  
Jian Zeng ◽  
Yan Yang
Keyword(s):  
Human Papillomavirus ◽  
Bacterial Community ◽  
Pregnant Women ◽  
Sequence Comparison ◽  
Pairwise Sequence Comparison ◽  
Vaginal Secretion ◽  
The Family ◽  
Complete Genomes ◽  
Different Types ◽  
Vaginal Tract

Abstract Background Although some studies have investigated the bacterial community in vaginal tract of pregnant women, there are few reports about the viral community (virome) in this type of microenvironment. Methods To investigate the composition of virome in vaginal secretion samples, 40 vaginal secretion samples from pregnant women with vaginitis and 20 vaginal secretion samples from pregnant women without vaginitis, pooled into 4 and 2 sample pools, respectively, were subjected to viral metagenomic analysis. Results Results indicated virus sequences showing similarity to human papillomavirus (HPV), anellovirus, and norovirus were recovered from this cohort of pregnant women. Further analysis indicated that 15 different defined types and one unclassified type of HPV were detected from pregnant women with vaginitis while only 3 defined types of HPV were detected in pregnant women without vaginitis. Five different groups of viruses from the family Anelloviridae were present in pregnant women with but none of them were detected in pregnant women without vaginitis. Norovirus was detected in 3 out of the 4 sample pools from pregnant women with vaginitis but none in the pregnant women without vaginitis. Twelve complete genomes belonging to 10 different types of HPV, and 5 novel anllovirus genomes belonging 2 different genera in Anelloviridae were acquired from these libraries, based on which phylogenetical analysis and pairwise sequence comparison were performed. Phageome in these samples was also briefly characterized and compared between two groups. Conclusion Our data suggested that virome might play an important role in the progression of vaginitis in pregnant women.

Positive selection of three chitinase genes of the family 18 of glycoside hydrolases in mammals

Biologia ◽  
2009 ◽  
Vol 64 (4) ◽  
Author(s):  
Beibei He ◽  
Li Wang ◽  
Jinhong Wang ◽  
Gang Li ◽  
Shuyi Zhang
Keyword(s):  
Positive Selection ◽  
Catalytic Domain ◽  
Digestive Enzyme ◽  
Glycoside Hydrolases ◽  
Wide Range ◽  
The Family ◽  
Maximum Likelihood Methods ◽  
Mammalian Genomes ◽  
Acidic Mammalian Chitinase ◽  
Chitinase Genes

AbstractThe digestive enzyme chitinase degrades chitin, and is found in a wide range of organisms, from prokaryotes to eukaryotes. Although mammals cannot synthesize or assimilate chitin, several proteins of the glycoside hydrolase (GH) chitinase family GH18, including some with enzymatic activity, have recently been identified from mammalian genomes. Consequently, there is growing interest in molecular evolution of this family of proteins. Here we report on the use of maximum likelihood methods to test for evidence of positive selection in three genes of the chitinase family GH18, all of which are found in mammals. These focal genes are CHIA, CHIT1 and CHI3L1, which encode the chitinase proteins acidic mammalian chitinase, chitotriosidase and cartilage protein 39, respectively. The results of our analyses indicate that each of these genes has undergone independent selective pressure in their evolution. Additionally, we have found evidence of a signature of positive natural selection, with most sites identified as being subject to adaptive evolution located in the catalytic domain. Our results suggest that positive selection on these genes stems from their function in digestion and/or immunity.

scholarly journals Distribution and Phylogenetic Analysis of Family 19 Chitinases in Actinobacteria

2004 ◽  
Vol 70 (2) ◽  
pp. 1135-1144 ◽  
Author(s):  
Tomokazu Kawase ◽  
Akihiro Saito ◽  
Toshiya Sato ◽  
Ryo Kanai ◽  
Takeshi Fujii ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Catalytic Domain ◽  
Higher Plants ◽  
Sequence Similarity ◽  
Evolutionary Relationship ◽  
Pcr Amplification ◽  
High Sequence Similarity ◽  
The Family ◽  
Family 19 Chitinase ◽  
Chitinase Genes

ABSTRACT In organisms other than higher plants, family 19 chitinase was first discovered in Streptomyces griseus HUT6037, and later, the general occurrence of this enzyme in Streptomyces species was demonstrated. In the present study, the distribution of family 19 chitinases in the class Actinobacteria and the phylogenetic relationship of Actinobacteria family 19 chitinases with family 19 chitinases of other organisms were investigated. Forty-nine strains were chosen to cover almost all the suborders of the class Actinobacteria, and chitinase production was examined. Of the 49 strains, 22 formed cleared zones on agar plates containing colloidal chitin and thus appeared to produce chitinases. These 22 chitinase-positive strains were subjected to Southern hybridization analysis by using a labeled DNA fragment corresponding to the catalytic domain of ChiC, and the presence of genes similar to chiC of S. griseus HUT6037 in at least 13 strains was suggested by the results. PCR amplification and sequencing of the DNA fragments corresponding to the major part of the catalytic domains of the family 19 chitinase genes confirmed the presence of family 19 chitinase genes in these 13 strains. The strains possessing family 19 chitinase genes belong to 6 of the 10 suborders in the order Actinomycetales, which account for the greatest part of the Actinobacteria. Phylogenetic analysis suggested that there is a close evolutionary relationship between family 19 chitinases found in Actinobacteria and plant class IV chitinases. The general occurrence of family 19 chitinase genes in Streptomycineae and the high sequence similarity among the genes found in Actinobacteria suggest that the family 19 chitinase gene was first acquired by an ancestor of the Streptomycineae and spread among the Actinobacteria through horizontal gene transfer.

scholarly journals CelI, a Noncellulosomal Family 9 Enzyme from Clostridium thermocellum, Is a Processive Endoglucanase That Degrades Crystalline Cellulose

2003 ◽  
Vol 185 (2) ◽  
pp. 391-398 ◽  
Author(s):  
Rachel Gilad ◽  
Larisa Rabinovich ◽  
Sima Yaron ◽  
Edward A. Bayer ◽  
Raphael Lamed ◽  
...  
Keyword(s):  
Clostridium Thermocellum ◽  
Catalytic Domain ◽  
Terminal Segment ◽  
Glycoside Hydrolases ◽  
General Nature ◽  
Crystalline Cellulose ◽  
Carbohydrate Binding ◽  
Truncated Form ◽  
Cellulose Substrates ◽  
The Family

ABSTRACT The family 9 cellulase gene celI of Clostridium thermocellum, was previously cloned, expressed, and characterized (G. P. Hazlewood, K. Davidson, J. I. Laurie, N. S. Huskisson, and H. J. Gilbert, J. Gen. Microbiol. 139:307-316, 1993). We have recloned and sequenced the entire celI gene and found that the published sequence contained a 53-bp deletion that generated a frameshift mutation, resulting in a truncated and modified C-terminal segment of the protein. The enzymatic properties of the wild-type protein were characterized and found to conform to those of other family 9 glycoside hydrolases with a so-called theme B architecture, where the catalytic module is fused to a family 3c carbohydrate-binding module (CBM3c); CelI also contains a C-terminal CBM3b. The intact recombinant CelI exhibited high levels of activity on all cellulosic substrates tested, with pH and temperature optima of 5.5 and 70°C, respectively, using carboxymethylcellulose as a substrate. Native CelI was capable of solubilizing filter paper, and the distribution of reducing sugar between the soluble and insoluble fractions suggests that the enzyme acts as a processive cellulase. A truncated form of the enzyme, lacking the C terminal CBM3b, failed to bind to crystalline cellulose and displayed reduced activity toward insoluble substrates. A truncated form of the enzyme, in which both the cellulose-binding CBM3b and the fused CBM3c were removed, failed to exhibit significant levels of activity on any of the substrates examined. This study underscores the general nature of this type of enzymatic theme, whereby the fused CBM3c plays a critical accessory role for the family 9 catalytic domain and changes its character to facilitate processive cleavage of recalcitrant cellulose substrates.

Relationship of the lateral embryo (in grasses) to other monocot embryos: a status up-grade

2021 ◽  
Vol 31 (3) ◽  
pp. 199-210
Author(s):  
Carol C. Baskin ◽  
Jerry M. Baskin
Keyword(s):  
Evolutionary Relationship ◽  
The Other ◽  
Family Tree ◽  
Seed Embryo ◽  
The Family ◽  
Relationship Of ◽  
Seed Characteristics

AbstractMartin placed the lateral embryo, which occurs only in grasses, adjacent to the broad embryo at the base of his family tree of seed phylogeny. Since Poales and Poaceae are derived monocots, we questioned the evolutionary relationship between the lateral embryo and other kinds of monocot embryos. Information was compiled on embryo and seed characteristics for the various families of monocots, kind of embryogenesis for families in Poales and germination morphology of families with lateral (only Poaceae) and broad embryos. The kinds of monocot embryos are broad, capitate, lateral, linear fully developed, linear underdeveloped and undifferentiated, but only broad and lateral embryos are restricted to Poales. Asterad embryogenesis occurs in Poaceae with a lateral embryo and in Eriocaulaceae, Rapataceae and Xyridaceae with a broad embryo. In developing grass seeds, the growing scutellum (cotyledon) pushes the coleoptile, mesocotyl and coleorhiza to the side. In the organless broad embryo, the cotyledonary sector is larger than the epicotyledonary sector. During germination of grass seeds, the coleorhiza and then the coleoptile emerge, while in a seed with a broad embryo the elongating cotyledon pushes the epicotyledonary sector outside the seed, after which a root–shoot axis is differentiated at a right angle to the cotyledon inside the seed. Broad and lateral embryos are closely related; however, the lateral embryo is more advanced in seed/embryo traits and germination morphology than the other kinds of monocot embryos, suggesting that its position on the family tree of seed phylogeny should be higher than of the other monocot embryos.

scholarly journals Dissecting molecular evolutionary relationship of Krameriaceae inferred from phylotranscriptomic analysis

2020 ◽  
Vol 27 (2) ◽  
pp. 427-433
Author(s):  
Mohammad Ajmal Ali ◽  
M Oliur Rahman ◽  
Joongku Lee ◽  
Fahad Al Hemaid ◽  
Sidanand V Kambhar ◽  
...  
Keyword(s):  
Evolutionary Relationship ◽  
Larrea Tridentata ◽  
Data Sets ◽  
Minimum Evolution ◽  
Likelihood Methods ◽  
The Family ◽  
Maximum Likelihood Methods ◽  
Plant Taxon ◽  
Systematic Relationships ◽  
Relationship Of

The systematic relationships of Krameriaceae have changed considerably. The phylotranscriptomic data sets provide highly informative data for resolving deeper‐level phylogenetic relationships. The phylotranscriptomic analyses to infer evolutionary relationships of Krameriaceae in the order Zygophyllales using the Minimum Evolution, Maximum Parsimony and Maximum Likelihood methods recovered similar topology and taxon proximity. Under the Zygophyllales clade, Krameria lanceolata Torr. of the family Krameriaceae nested with Tribulus eichlerianus K.L. Wilson and Larrea tridentata (Sessé & Moc. ex DC.) Coville belonging to the family Zygophyllaceae with strong nodal support. The phylotranscriptomic analyses suggest that the family Krameriaceae is sister to Zygophyllaceae. Bangladesh J. Plant Taxon. 27(2): 427-433, 2020 (December)

Hubungan Sikap dan Karakteristik Pasangan Usia Subur (PUS) dengan Keikutsertaan dalam Program KB di Wilayah Kerja UPT Puskesmas Sungai Raya Kecamatan Sungai Raya Kabupaten Aceh Timur

2020 ◽  
Vol 8 (2) ◽  
pp. 105-114
Author(s):  
Ainul Mardhiah ◽  
Nova Hasbani Prima Dewi ◽  
Aminy Aminy
Keyword(s):  
Family Planning ◽  
Family Planning Program ◽  
The Elderly ◽  
P Value ◽  
Planning Program ◽  
Elderly Age ◽  
Chi Square ◽  
Cross Sectional ◽  
The Family ◽  
Relationship Of

The family planning program also aims to improve the quality of the family in order to generate a sense of security, peace and hope of a better future in realizing the prosperity of birth and inner happiness. Allegedly the factor causing EFA participation in the family planning program is characteristic. The purpose of this research is to know the relationship of attitude and characteristic of Elderly Age Couple (PUS) with participation in family planning program at UPT Puskesmas Sungai Raya Sungai Raya District, East Aceh regency 2018. The research design used was analytic survey with cross sectional design. The population of this study is all Pairs Age of Fertile located in Work Area UPT Sungai Raya Public Health Service Center in January to December 2017 which amounted to 1897 people. Sampling using Slovin formula, obtained as many as 95 samples. The study was conducted from 7-17 July 2018 using questionnaires by interview. Statistical test using chi-square test. Result of research indicate that majority of fertile couple couples (PUS) participate in family planning program as much as 67 respondents (70,5%). Statistically there is relationship of attitude and characteristic of Elderly Age Couple (EFA) with non participation in family planning program in Working Area of UPT Puskesmas Sungai Raya Sungai Raya District of East Aceh Regency 2018 with p value <0,1. It is recommended that the family planning program holders in UPT Puskesmas Sungai Raya Sungai Raya District of East Aceh District to invite cross-sectoral figures to hold meetings to create mini workshop plans at least once a month to increase the participation of the Elderly Age Couple (PUS) in family planning programs. Keyword : Family Planning Program, Attitudes, CharacteristicsABSTRAKProgram KB juga bertujuan untuk meningkatkan kualitas keluarga agar dapat timbul rasa aman, tentram, dan harapan masa depan yang lebih baik dalam mewujudkan kesejahteraan lahir dan kebahagiaan batin. Diduga faktor yang menyebabkan ketidakikutsertaan PUS dalam program KB adalah karakteristik. Tujuan penelitian ini untuk mengetahui hubungan sikap dan karakteristik Pasangan Usia Subur (PUS) dengan keikutsertaan dalam program KB di Wilayah Kerja UPT Puskesmas Sungai Raya Kecamatan Sungai Raya Kabupaten Aceh Timur tahun 2018. Desain penelitian yang digunakan adalah survei analitik dengan rancangan bedah lintang. Populasi dari penelitian ini adalah seluruh Pasangan Usia Subur yang berada di Wilayah Kerja UPT Puskesmas Sungai Raya pada bulan Januari sampai dengan Desember tahun 2017 yang berjumlah 1.897 orang. Pengambilan sampel menggunakan rumus Slovin, didapatkan sebanyak 95 sampel. Penelitian dilaksanakan dari tanggal 7-17 Juli tahun 2018 menggunakan kuesioner dengan cara wawancara. Uji statistik menggunakan uji chi-square. Hasil penelitian menunjukkan bahwa mayoritas Pasangan Usia Subur (PUS) ikut serta dalam program KB yaitu sebanyak 67 responden (70,5%). Secara statistik ada hubungan sikap dan karakteristik Pasangan Usia Subur (PUS) dengan ketidakikutsertaan dalam program KB di Wilayah Kerja UPT Puskesmas Sungai Raya Kecamatan Sungai Raya Kabupaten Aceh Timur tahun 2018 dengan p value < 0,1. Sebaiknya pemegang program KB di UPT Puskesmas Sungai Raya Kecamatan Sungai Raya Kabupaten Aceh Timur agar mengajak tokoh lintas sektor agar mengadakan pertemuan untuk membuat rencana loka karya mini setidaknya satu bulan sekali untuk meningkatkan keikutsertaan Pasangan Usia Subur (PUS) dalam program KB.Kata Kunci : Program KB, Sikap, Karakteristik

Morphological re-description and phylogenetic relationship of five myxosporean species of the family Myxobolidae infecting Nile tilapia

2017 ◽  
Vol 124 (3) ◽  
pp. 201-214 ◽  
Author(s):  
R Abdel-Gaber ◽  
F Abdel-Ghaffar ◽  
S Maher ◽  
AM El-Mallah ◽  
S Al Quraishy ◽  
...  
Keyword(s):  
Phylogenetic Relationship ◽  
Nile Tilapia ◽  
The Family ◽  
Relationship Of ◽  
Myxosporean Species

Phylogeny of actin and tubulin gene homologs in diverse eukaryotic species

2019 ◽  
Vol 79 (01S) ◽  
Author(s):  
Pawan Kumar Jayaswal ◽  
Asheesh Shanker ◽  
Nagendra Kumar Singh
Keyword(s):  
Evolutionary Relationship ◽  
Genomic Data ◽  
Gene Clusters ◽  
Species Trees ◽  
Model Species ◽  
Tubulin Gene ◽  
Tubulin Genes ◽  
Eukaryotic Species ◽  
Relationship Of ◽  
Insight Into

Actin and tubulin are cytoskeleton proteins, which are important components of the celland are conserved across species. Despite their crucial significance in cell motility and cell division the distribution and phylogeny of actin and tubulin genes across taxa is poorly understood. Here we used publicly available genomic data of 49 model species of plants, animals, fungi and Protista for further understanding the distribution of these genes among diverse eukaryotic species using rice as reference. The highest numbers of rice actin and tubulin gene homologs were present in plants followed by animals, fungi and Protista species, whereas ten actin and nine tubulin genes were conserved in all 49 species. Phylogenetic analysis of 19 actin and 18 tubulin genes clustered them into four major groups each. One each of the actin and tubulin gene clusters was conserved across eukaryotic species. Species trees based on the conserved actin and tubulin genes showed evolutionary relationship of 49 different taxa clustered into plants, animals, fungi and Protista. This study provides a phylogenetic insight into the evolution of actin and tubulin genes in diverse eukaryotic species.

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