Journal of Genetics and Genomics

Number matters: control of mammalian mitochondrial DNA copy number

Laura L. Clay Montier, Janice J. Deng, Yidong Bai

2009, 36(3): 125-131. doi: 10.1016/S1673-8527(08)60099-5

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Abstract:
Regulation of mitochondrial biogenesis is essential for proper cellular functioning. Mitochondrial DNA (mtDNA) depletion and the resulting mitochondrial malfunction have been implicated in cancer, neurodegeneration, diabetes, aging, and many other human diseases. Although it is known that the dynamics of the mammalian mitochondrial genome are not linked with that of the nuclear genome, very little is known about the mechanism of mtDNA propagation. Nevertheless, our understanding of the mode of mtDNA replication has advanced in recent years, though not without some controversies. This review summarizes our current knowledge of mtDNA copy number control in mammalian cells, while focusing on both mtDNA replication and turnover. Although mtDNA copy number is seemingly in excess, we reason that mtDNA copy number control is an important aspect of mitochondrial genetics and biogenesis and is essential for normal cellular function.

Differentiation potential of bone marrow mesenchymal stem cells in duck

Linfeng Li, Xiujuan Bai, Xuelian Gong, Hongkun Liu, Lina Chen, Weijun Guan, Yuehui Ma

2009, 36(3): 133-140. doi: 10.1016/S1673-8527(08)60100-9

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The bone marrow mesenchymal stem cells (MSCs) are multipotent stem cells which can differentiate into mesenchymal cellsin vitro. In this study, MSCs in duck were isolated from bone marrow by density gradient centrifuge separation, purified and expanded in the medium. The primary MSCs were expanded for passages. The different-passage MSCs were induced to differentiate into osteoblasts and neuron-like cells. Karyotype analysis indicated that MSCs kept diploid condition and the hereditary feature was stable. The different-passage MSCs expressed CD44, ICAM- and SSEA-4, but not CD34, CD45 and SSEA-when detected by immunofluorescence staining. There was no significant difference among the positive rates of passages 2, 6 and 8 (P > 0.05), but a significant difference existed among those of passages 2, 6, 8 and 11 ( P < 0.05). After the osteogenic inducement was added, the induced different-passage MSCs expressed high-level alkaline phosphatase (ALP), and are positive for tetracycline staining, Alizarin Red staining and Von Kossa staining. After the neural inducement was added, about 70% cells exhibited typical neuron-like phenotype, the induced different-passage MSCs expressed Nestin, neuron-specific enolase (NSE) and glial fibrillary acidic protein (GFAP) when detected by immunofluorescence staining. There was no significant difference among the positive rates of passages 3, 4 and 6 ( P>0.05), but a significant difference existed among those of passages 3, 4, 6 and 8 (P<0.05). These results suggest that MSCs in duck were capable of differentiating into osteoblasts and neuron-like cellsin vitro.

Cotton GhPOX1 encoding plant class III peroxidase may be responsible for the high level of reactive oxygen species production that is related to cotton fiber elongation

Wenqian Mei, Yongmei Qin, Wenqiang Song, Jun Li, Yuxian Zhu

2009, 36(3): 141-150. doi: 10.1016/S1673-8527(08)60101-0

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The accumulation of reactive oxygen species (ROS) is involved in plant cell development. In plant, class III peroxidases are heme-containing enzymes encoded by a large multi-gene family participated in the release or consumption of ROS. The specific function of each member of the family is still elusive. Here, we showed that ROS was significantly generated during cotton fiber initiation and elongation, whereas, application of NADPH oxidase inhibitor diphenyleneiodonium (DPI) and peroxidase inhibitor salicylhydroxamic acid (SHAM) to the wild-type cotton ovule culture significantly suppressed fiber growth, respectively. Their inhibitory effects were caused by the reduction of superoxide radical (O₂⁻). Ten GhPOX genes (cDNAs) encoding cotton class III peroxidases were isolated, among them eight GhPOX genes were reported for the first time. Microarray analyses indicated that GhPOX1 was the mostly predominantly expressed in fast-elongating cotton fiber cells. Real-time quantitative PCR analysis revealed the transcript level of GhPOX1 was over 400-fold higher in growing fiber cells than in ovules, flowers, roots, stems and leaves. To reveal the role of GhPOX1 in plant development, its Arabidopsis orthologue atpox13 mutant was demonstrated to be defective in branch root development. Taken together, the data suggest that GhPOX1 plays an important role during fiber cell elongation possibly by mediating production of reactive oxygen species.

Revaluation of deuterostome phylogeny and evolutionary relationships among chordate subphyla using mitogenome data

Jing Zhong, Juyong Zhang, Emmanuel Mukwaya, Yiquan Wang

2009, 36(3): 151-160. doi: 10.1016/S1673-8527(08)60102-2

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The traditional knowledge in textbooks indicated that cephalochordates were the closest relatives to vertebrates among all extant organisms. However, this opinion was challenged by several recent phylogenetic studies using hundreds of nuclear genes. The researchers suggested that urochordates, but not cephalochordates, should be the closest living relatives to vertebrates. In the present study, by using data generated from hundreds of mtDNA sequences, we revalue the deuterostome phylogeny in terms of whole mitochondrial genomes (mitogenomes). Our results firmly demonstrate that each of extant deuterostome phyla and chordate subphyla is monophyletic. But the results present several alternative phylogenetic trees depending on different sequence datasets used in the analysis. Although no clear phylogenetic relationships are obtained, those trees indicate that the ancient common ancestor diversified rapidly soon after their appearance in the early Cambrian and generated all major deuterostome lineages during a short historical period, which is consistent with “Cambrian explosion” revealed by paleontologists. It was the 520-million-year's evolution that obscured the phylogenetic relationships of extant deuterostomes. Thus, we conclude that an integrative analysis approach rather than simply using more DNA sequences should be employed to address the distant evolutionary relationship.

Molecular evolution and functional divergence of HAK potassium transporter gene family in rice (Oryza sativa L.)

Zefeng Yang, Qingsong Gao, Changsen Sun, Wenjuan Li, Shiliang Gu, Chenwu Xu

2009, 36(3): 161-172. doi: 10.1016/S1673-8527(08)60103-4

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The high-affinity K⁺ (HAK) transporter gene family is the largest family in plant that functions as potassium transporter and is important for various aspects of plant life. In the present study, we identified 27 members of this family in rice genome. The phylogenetic tree divided the land plant HAK transporter proteins into 6 distinct groups. Although the main characteristic of this family was established before the origin of seed plants, they also showed some differences between the members of non-seed and seed plants. The HAK genes in rice were found to have expanded in lineage-specific manner after the split of monocots and dicots, and both segmental duplication events and tandem duplication events contributed to the expansion of this family. Functional divergence analysis for this family provided statistical evidence for shifted evolutionary rate after gene duplication. Further analysis indicated that both point mutant with positive selection and gene conversion events contributed to the evolution of this family in rice.

Root and shoot traits responses to phosphorus deficiency and QTL analysis at seedling stage using introgression lines of rice

Junzhou Li, Yan Xie, Anyong Dai, Lifeng Liu, Zichao Li

2009, 36(3): 173-183. doi: 10.1016/S1673-8527(08)60104-6

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Phosphorous (P) deficiency is a major restraint factor for crop production and plants have developed several mechanisms to adapt to low P stress. In this study, a set of 271 introgression lines (ILs) were used to characterize the responses of seedlings to low P availability and to identify QTLs for root traits, biomass, and plant height under P-deficiency and P-sufficiency conditions. Plant height, total dry weight, shoot dry weight, and root number were inhibited under P-deficiency, whereas maximum root length (MRL) and root-shoot ratio (RS) were induced by P-deficiency stress. Relative MRL (RMRL, the ratio of MRL under P-deficiency to MRL under P-sufficiency condition) and relative RS (RRS) were used to evaluate P-deficiency tolerance at the seedling stage. A total of 24 additive QTLs and 29 pairs of epistatic QTLs were detected, but only qRN4 was detected in both conditions. This suggested that different mechanisms may exist in both P supply levels. QTLs for adaptive traits (RMRL, RRS, RRV, and RRDW) and qRN4 consistently expressed to increase trait stability may contribute to P-deficiency tolerance. Twelve intervals were cluster regions of QTLs for P-deficiency tolerance, and one QTL (qRRS8) showed pleiotropic effects on P-deficiency tolerance and drought tolerance. These interesting QTLs can be used in marker-assisted breeding through the target ILs.

21st IUBMB and 12th FAOBMB International Congress of Biochemistry and Molecular Biology

2009, 36(3) doi: 10.1016/S1673-8527(09)60008-4

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Instructions for authors

2009, 36(3): 185-188. doi: 10.1016/S1673-8527(09)60009-6

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2009 Vol. 36, No. 3