Identification and Expression Analysis of profilin Gene Family in Hevea brasiliensis

doi:10.3969/j.issn.1000-2561.2021.09.002

Abstract

Abstract:

Actin cytoskeleton might play an important role in laticifer wound plugging of Hevea brasiliensis. Although profilin is a vital regulator in actin dynamics, there is still no systematic study on profilin gene family in Hevea brasiliensis. In this study, six profilin genes were identified from the genome and transcriptome of Hevea brasiliensis. The six genes were analyzed in details, including gene basic characteristics, conserved protein motifs, structure features, evolutionary relationships, and expression profiles. Gene structure analyses demonstrated that the six profilin genes contained three exons and two introns. Conserved domain analyses indicated that the six profilin proteins possessed unique motifs of profilin protein, KYMVIQGE and VIRGKKG motifs. Evolutionary analyses showed that Hevea profilins were not strictly divided into vegetative and reproductive subclasses. The main secondary structures of profilin proteins were random coil and tertiary structures consist of three α helices and seven β turns. Expression analyses showed that four profilin genes were highly expressed in latex, and regulated by latex flow and potassium iodide treatment, suggesting that profilin genes might be involved in latex flow. These results would lay a foundation for further elucidating profilin roles in laticifer wound plugging and latex flow of Hevea brasiliensis.

Key words: Profilin gene family, Hevea brasiliensis, latex flow, expression analysis

CLC Number:

S794.1

DENG Zhi, LI Dejun. Identification and Expression Analysis of profilin Gene Family in Hevea brasiliensis[J]. Chinese Journal of Tropical Crops, 2021, 42(9): 2443-2450.

Figures/Tables 10

Tab. 1 qRT-PCR primers in this study

基因名称 Gene name	正向引物（5′-3′） Forward primer (5′-3′)	反向引物（5′-3′） Reverse primer (5′-3′)
HbPRF1	CACAGAAGCAAAGCGAGCCT	CGGCAGCAGAGAGATGATTG
HbPRF2	AAGCTTCATCAAATCTCTGA	TGAGGGAAGTTGGAGCTCTG
HbPRF4	GGGATCAACGGTTACGATTTG	ACTGAGGGAAGCTGGAGCTCT
HbPRF6	GGATAAAATGTCGTGGCAAAC	ATACGCTACCATCATGGCCA
Hb18S rRNA	GCTCGAAGACGATCAGATACC	TTCAGCCTTGCGACCATAC

Tab. 2 Identification of profilin genes in H. brasiliensis

基因名称 Gene name	基因ID Gene ID	开放阅读框长度 Length of open reading frame/bp	氨基酸数目 Number of amino acids/aa	分子量 Molecular weight/kDa	等电点 Isoelectric point	总平均亲水性 Grand average of hydropathicity	不稳定系数 Instability index
HbPRF1	scaffold0108_721523	396	131	14.13	4.71	-0.123	29.52
HbPRF2	scaffold1375_37486	396	131	14.13	4.63	-0.141	31.18
HbPRF3	scaffold1290_97794	396	131	14.07	5.00	-0.098	30.19
HbPRF4	scaffold2144_14700	396	131	14.00	4.97	-0.101	25.41
HbPRF5	scaffold0108_718468	402	133	14.33	5.02	-0.185	27.18
HbPRF6	scaffold1375_41318	402	133	14.35	5.02	-0.205	27.18

Fig.1 Sequence alignment of profilin protein from H. brasiliensis Horizontal lines represent the conserved motif of profilin protein.

Fig. 2 Gene structures of profilin genes from H. brasiliensis Blue boxes and black lines represent the exons and introns, respectively.

Tab. 3 Secondary structure of profilin proteins from H. brasilinesis

蛋白名称 Profilin name	α螺旋比例 Ratio of α-Helix/%	β折叠比例 Ratio of β fold/%	延伸链比例 Ratio of extended chain /%	无规则卷曲比例 Ratio of random coil/%
HbPRF1	22.14	10.69	25.19	41.98
HbPRF2	26.72	8.40	25.19	39.69
HbPRF3	26.72	6.87	25.19	41.22
HbPRF4	27.48	9.16	23.66	39.69
HbPRF5	26.32	9.77	23.31	40.60
HbPRF6	30.83	9.77	24.06	35.34

Fig. 3 3D structure prediction of profilin proteins of H. brasiliensis

Fig. 4 Phylogenetic analysis of plant profilin proteins AtPRF1~AtPRF5: Arabidopsis thaliana (AAB39480.1, AAB39481.1, Q9FE63.2, AAB39477.1, AAB39479.1); OsPRF1~OsPRF2: Oryza sativa (BAD69332.1, AAK92580.1); ZmPRF1~ZmPRF6: Zea mays (CAA51718.1, CAA51719.1, CAA51720.1, AAB86960.1, AAG35601.1, ONM38364.1);PtPRF1~PtPRF3: Populus trichocarpa (XP_002304225.1, XP_002299743.1, XP_011000942.1); VvPRF1~VvPRF4: Vitis vinifera (XP_002274966.3, XP_002283450.1, XP_002283490.1, XP_010656249.1); JcPRF1~JcPRF3: Jatropha curcas (NP_001295719.1, XP_012069066.1, XP_012076840.1); RcPRF1~RcPRF3: Ricinus communis (XP_002514199.1, XP_002515952.1, XP_002514198.1); CcPRF: Colletotrichum chlorophyti (OLN95629).

Fig. 5 Tissue expression profiles of profilin from H. brasilinesis

Fig. 6 Expression profiles of four HbPRFs under different different time of latex flow T1: 0-5 min after tapping; T2: >5-35 min after tapping; T3: >35 min after tapping until rubber discharge stop.

Fig. 7 Expression profiles of four HbPRFs under KI treatment

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