Reflections on the tissue kallikrein and kallikrein-related peptidase family – from mice to men – what have we learnt in the last two decades?

2008 ◽  
Vol 389 (12) ◽  
Author(s):  
Judith A. Clements
Keyword(s):  
Hormonal Regulation ◽  
Expression Patterns ◽  
Gene Families ◽  
Lessons Learned ◽  
Current Status ◽  
Tissue Kallikrein ◽  
Genes Encoding ◽  
Exciting Source ◽  
Encoding Gene ◽  
New Biomarkers

AbstractThe genes encoding the kininogenase, glandular tissue kallikrein, in rodents and man were first described in the mid-1980s. Remarkably, they appeared to be part of a much larger highly conserved family of genes (GK) in rodents, but only had two paralogs in man. This discrepancy was not rectified until the late 1990s/2000 with the identification of a cluster of 12 more kallikrein-related (KLK) genes in the human 19q13 locus and the subsequent identification of their rodent homologs. Interestingly, there are remarkable similarities in expression patterns, hormonal regulation and functional attributes of the old (GK) and new (KLK) families which underscore the evolutionary conservation across these loci and species. This historical perspective focuses on the lessons learned from earlier studies on the rodentGKgene families and the striking similarities of some attributes, yet uniqueness, of others. These earlier findings have all contributed to the current status of the KLK serine peptidase-encoding gene family as an exciting source of new biomarkers and therapeutic targets.

Variability among members of the Hor-2 multigene family

Genome ◽  
1993 ◽  
Vol 36 (3) ◽  
pp. 397-403 ◽  
Author(s):  
Vladimir Kanazin ◽  
Evgeny Ananiev ◽  
Tom Blake
Keyword(s):  
Polymerase Chain Reaction ◽  
Gene Family ◽  
Storage Proteins ◽  
Gene Families ◽  
Reaction Sequence ◽  
Chain Reaction ◽  
Genes Encoding ◽  
Polymerase Chain ◽  
Encoding Gene ◽  
Barley Genotypes

The hordeins comprise the major prolamin storage proteins of barley. Two major and one minor gene families encode these alcohol-soluble proteins. The Hor-2 gene family encoding the B-hordeins has been estimated to contain 15–30 copies. Although several genes encoding B-hordeins have been cloned and sequenced, little is known about the mechanisms responsible for the generation of the enormous genetic variability at this locus. Polymerase chain reaction sequence amplification provided a simple technique that permitted the amplification of the Hor-2 gene family members from the genomes of several barley genotypes. Sequence analysis of clones permitted the identification of a region within the Hor-2 structural gene that appears to undergo recombinational and slippage-like gene conversion events. In this report we describe variability of the B-hordein genes, possible mechanisms responsible for it, and implications this may have on the evolution of prolamin-encoding gene families.Key words: barley, hordeins, polymerase chain reaction, polymorphism.

scholarly journals Recent Duplications Dominate VQ and WRKY Gene Expansions in Six Prunus Species

2021 ◽  
Vol 2021 ◽  
pp. 1-16
Author(s):  
Yan Zhong ◽  
Ping Wang ◽  
Xiaohui Zhang ◽  
Zong-Ming Cheng
Keyword(s):  
Stress Responses ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Gene Families ◽  
Wrky Gene ◽  
Prunus Species ◽  
Gene Copies ◽  
Genes Encoding ◽  
Tree Topologies ◽  
The Common

Genes encoding VQ motif-containing (VQ) transcriptional regulators and WRKY transcription factors can participate separately or jointly in plant growth, development, and abiotic and biotic stress responses. In this study, 222 VQ and 645 WRKY genes were identified in six Prunus species. Based on phylogenetic tree topologies, the VQ and WRKY genes were classified into 13 and 32 clades, respectively. Therefore, at least 13 VQ gene copies and 32 WRKY gene copies were present in the genome of the common ancestor of the six Prunus species. Similar small Ks value peaks for the VQ and WRKY genes suggest that the two gene families underwent recent duplications in the six studied species. The majority of the Ka/Ks ratios were less than 1, implying that most of the VQ and WRKY genes had undergone purifying selection. Pi values were significantly higher in the VQ genes than in the WRKY genes, and the VQ genes therefore exhibited greater nucleotide diversity in the six species. Forty-one of the Prunus VQ genes were predicted to interact with 44 of the WRKY genes, and the expression levels of some predicted VQ-WRKY interacting pairs were significantly correlated. Differential expression patterns of the VQ and WRKY genes suggested that some might be involved in regulating aphid resistance in P. persica and fruit development in P. avium.

Heat shock genes and the heat shock response in zebrafish embryos

1997 ◽  
Vol 75 (5) ◽  
pp. 487-497 ◽  
Author(s):  
Patrick H Krone ◽  
Zsolt Lele ◽  
Jennifer B Sass
Keyword(s):  
Heat Shock ◽  
Embryonic Development ◽  
Expression Patterns ◽  
Gene Families ◽  
Zebrafish Embryos ◽  
Heat Shock Genes ◽  
Specific Expression ◽  
Temporal Regulation ◽  
Wide Range ◽  
Genes Encoding

Heat shock genes exhibit complex patterns of spatial and temporal regulation during embryonic development in a wide range of organisms. Our laboratory has initiated an analysis of heat shock protein gene expression in the zebrafish, a model system that is now utilized extensively for the examination of early embryonic development of vertebrates. We have cloned members of the zebrafish hsp47, hsp70,\i and hsp90 gene families and shown them to be closely related to their counterparts in higher vertebrates. Whole mount in situ hybridization and Northern blot analyses have revealed that these genes are regulated in distinct spatial, temporal, and stress-specific manners. Furthermore, the tissue-specific expression patterns of the hsp47 and hsp90 alpha genes correlate closely with the expression of genes encoding known chaperone targets of Hsp47 and Hsp90 in other systems. The data raise a number of interesting questions regarding the function and regulation of these heat shock genes in zebrafish embryos during normal development and following exposure to environmental stress.

Insights into the heat-responsive transcriptional network of tomato contrasting genotypes

2021 ◽  
Vol 19 (1) ◽  
pp. 44-57
Author(s):  
Sirine Werghi ◽  
Charfeddine Gharsallah ◽  
Nishi Kant Bhardwaj ◽  
Hatem Fakhfakh ◽  
Faten Gorsane
Keyword(s):  
Heat Stress ◽  
Heat Shock ◽  
Candidate Genes ◽  
Expression Patterns ◽  
Response Strategies ◽  
Transcriptional Reprogramming ◽  
Genes Encoding ◽  
Breeding Programmes ◽  
Gene Transcripts ◽  
Resource Data

AbstractDuring recent decades, global warming has intensified, altering crop growth, development and survival. To overcome changes in their environment, plants undergo transcriptional reprogramming to activate stress response strategies/pathways. To evaluate the genetic bases of the response to heat stress, Conserved DNA-derived Polymorphism (CDDP) markers were applied across tomato genome of eight cultivars. Despite scattered genotypes, cluster analysis allowed two neighbouring panels to be discriminate. Tomato CDDP-genotypic and visual phenotypic assortment permitted the selection of two contrasting heat-tolerant and heat-sensitive cultivars. Further analysis explored differential expression in transcript levels of genes, encoding heat shock transcription factors (HSFs, HsfA1, HsfA2, HsfB1), members of the heat shock protein (HSP) family (HSP101, HSP17, HSP90) and ascorbate peroxidase (APX) enzymes (APX1, APX2). Based on discriminating CDDP-markers, a protein functional network was built allowing prediction of candidate genes and their regulating miRNA. Expression patterns analysis revealed that miR156d and miR397 were heat-responsive showing a typical inverse relation with the abundance of their target gene transcripts. Heat stress is inducing a set of candidate genes, whose expression seems to be modulated through a complex regulatory network. Integrating genetic resource data is required for identifying valuable tomato genotypes that can be considered in marker-assisted breeding programmes to improve tomato heat tolerance.

scholarly journals Two Auxinic Herbicides Affect Brassica napus Plant Hormone Levels and Induce Molecular Changes in Transcription

Biomolecules ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1153
Author(s):  
Jutta Ludwig-Müller ◽  
Roman Rattunde ◽  
Sabine Rößler ◽  
Katja Liedel ◽  
Freia Benade ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Expression Patterns ◽  
Growth Conditions ◽  
Growth Stages ◽  
Auxin Response ◽  
Time Points ◽  
Genes Encoding ◽  
Different Temperatures ◽  
Indigenous Plant ◽  
Over Time

With the introduction of the new auxinic herbicide halauxifen-methyl into the oilseed rape (Brassica napus) market, there is a need to understand how this new molecule interacts with indigenous plant hormones (e.g., IAA) in terms of crop response. The aim of this study was to investigate the molecular background by using different growth conditions under which three different auxinic herbicides were administered. These were halauxifen-methyl (Hal), alone and together with aminopyralid (AP) as well as picloram (Pic). Three different hormone classes were determined, free and conjugated indole-3-acetic acid (IAA), aminocyclopropane carboxylic acid (ACC) as a precursor for ethylene, and abscisic acid (ABA) at two different temperatures and growth stages as well as over time (2–168 h after treatment). At 15 °C growth temperature, the effect was more pronounced than at 9 °C, and generally, the younger leaves independent of the developmental stage showed a larger effect on the alterations of hormones. IAA and ACC showed reproducible alterations after auxinic herbicide treatments over time, while ABA did not. Finally, a transcriptome analysis after treatment with two auxinic herbicides, Hal and Pic, showed different expression patterns. Hal treatment leads to the upregulation of auxin and hormone responses at 48 h and 96 h. Pic treatment induced the hormone/auxin response already after 2 h, and this continued for the other time points. The more detailed analysis of the auxin response in the datasets indicate a role for GH3 genes and genes encoding auxin efflux proteins. The upregulation of the GH3 genes correlates with the increase in conjugated IAA at the same time points and treatments. Also, genes for were found that confirm the upregulation of the ethylene pathway.

scholarly journals Arabidopsis Genes Essential for Seedling Viability: Isolation of Insertional Mutants and Molecular Cloning

Genetics ◽  
2001 ◽  
Vol 159 (4) ◽  
pp. 1765-1778
Author(s):  
Gregory J Budziszewski ◽  
Sharon Potter Lewis ◽  
Lyn Wegrich Glover ◽  
Jennifer Reineke ◽  
Gary Jones ◽  
...  
Keyword(s):  
Large Scale ◽  
Protein Translocation ◽  
Gene Families ◽  
Mutant Phenotype ◽  
Lethal Mutant ◽  
A Genome ◽  
Genes Encoding ◽  
High Level ◽  
Mutant Lines ◽  
Genome Scale

Abstract We have undertaken a large-scale genetic screen to identify genes with a seedling-lethal mutant phenotype. From screening ~38,000 insertional mutant lines, we identified >500 seedling-lethal mutants, completed cosegregation analysis of the insertion and the lethal phenotype for >200 mutants, molecularly characterized 54 mutants, and provided a detailed description for 22 of them. Most of the seedling-lethal mutants seem to affect chloroplast function because they display altered pigmentation and affect genes encoding proteins predicted to have chloroplast localization. Although a high level of functional redundancy in Arabidopsis might be expected because 65% of genes are members of gene families, we found that 41% of the essential genes found in this study are members of Arabidopsis gene families. In addition, we isolated several interesting classes of mutants and genes. We found three mutants in the recently discovered nonmevalonate isoprenoid biosynthetic pathway and mutants disrupting genes similar to Tic40 and tatC, which are likely to be involved in chloroplast protein translocation. Finally, we directly compared T-DNA and Ac/Ds transposon mutagenesis methods in Arabidopsis on a genome scale. In each population, we found only about one-third of the insertion mutations cosegregated with a mutant phenotype.

scholarly journals Comprehensive Analysis of the Histone Deacetylase Gene Family in Chinese Cabbage (Brassica rapa): From Evolution and Expression Pattern to Functional Analysis of BraHDA3

Agriculture ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 244
Author(s):  
Seung Hee Eom ◽  
Tae Kyung Hyun
Keyword(s):  
Functional Analysis ◽  
Brassica Rapa ◽  
Chinese Cabbage ◽  
Stress Responses ◽  
Histone Deacetylases ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Gene Families ◽  
Physiological Processes ◽  
Lysine Residues

Histone deacetylases (HDACs) are known as erasers that remove acetyl groups from lysine residues in histones. Although plant HDACs play essential roles in physiological processes, including various stress responses, our knowledge concerning HDAC gene families and their evolutionary relationship remains limited. In Brassica rapa genome, we identified 20 HDAC genes, which are divided into three major groups: RPD3/HDA1, HD2, and SIR2 families. In addition, seven pairs of segmental duplicated paralogs and one pair of tandem duplicated paralogs were identified in the B. rapa HDAC (BraHDAC) family, indicating that segmental duplication is predominant for the expansion of the BraHDAC genes. The expression patterns of paralogous gene pairs suggest a divergence in the function of BraHDACs under various stress conditions. Furthermore, we suggested that BraHDA3 (homologous of Arabidopsis HDA14) encodes the functional HDAC enzyme, which can be inhibited by Class I/II HDAC inhibitor SAHA. As a first step toward understanding the epigenetic responses to environmental stresses in Chinese cabbage, our results provide a solid foundation for functional analysis of the BraHDAC family.

scholarly journals Identification and Expression Analysis of the Genes Involved in the Raffinose Family Oligosaccharides Pathway of Phaseolus vulgaris and Glycine max

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1465
Author(s):  
Ramon de Koning ◽  
Raphaël Kiekens ◽  
Mary Esther Muyoka Toili ◽  
Geert Angenon
Keyword(s):  
Common Bean ◽  
Seed Development ◽  
Expression Analysis ◽  
De Novo ◽  
Expression Patterns ◽  
Gene Families ◽  
Rna Seq ◽  
Raffinose Family Oligosaccharides ◽  
Specific Expression ◽  
Raffinose Synthase

Raffinose family oligosaccharides (RFO) play an important role in plants but are also considered to be antinutritional factors. A profound understanding of the galactinol and RFO biosynthetic gene families and the expression patterns of the individual genes is a prerequisite for the sustainable reduction of the RFO content in the seeds, without compromising normal plant development and functioning. In this paper, an overview of the annotation and genetic structure of all galactinol- and RFO biosynthesis genes is given for soybean and common bean. In common bean, three galactinol synthase genes, two raffinose synthase genes and one stachyose synthase gene were identified for the first time. To discover the expression patterns of these genes in different tissues, two expression atlases have been created through re-analysis of publicly available RNA-seq data. De novo expression analysis through an RNA-seq study during seed development of three varieties of common bean gave more insight into the expression patterns of these genes during the seed development. The results of the expression analysis suggest that different classes of galactinol- and RFO synthase genes have tissue-specific expression patterns in soybean and common bean. With the obtained knowledge, important galactinol- and RFO synthase genes that specifically play a key role in the accumulation of RFOs in the seeds are identified. These candidate genes may play a pivotal role in reducing the RFO content in the seeds of important legumes which could improve the nutritional quality of these beans and would solve the discomforts associated with their consumption.

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